HEADER DNA BINDING PROTEIN 01-AUG-24 9IZR TITLE CRYO-EM STRUCTURE OF CASLAMBDA2-CRRNA-TARGET DNA TERNARY COMPLEX IN TITLE 2 THE NTS-CLEAVING STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAS LAMBDA2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (58-MER); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (40-MER); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA (40-MER); COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 3 ORGANISM_TAXID: 32644; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 8 ORGANISM_TAXID: 32644; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 13 ORGANISM_TAXID: 32644; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 MOL_ID: 4; SOURCE 17 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 18 ORGANISM_TAXID: 32644; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CRISPR-CAS12, GENOME ENGINEERING, HYDROLASE-RNA-DNA COMPLEX, DNA KEYWDS 2 BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.N.OMURA,H.HIRANO,Y.ITOH,O.NUREKI REVDAT 2 25-JUN-25 9IZR 1 JRNL REVDAT 1 11-JUN-25 9IZR 0 JRNL AUTH S.N.OMURA,L.E.ALFONSE,A.ORNSTEIN,H.MORINAGA,H.HIRANO,Y.ITOH, JRNL AUTH 2 G.MUNOZ,A.J.GARRITY,G.R.HOFFMAN,T.DITOMMASO,W.X.YAN, JRNL AUTH 3 D.R.CHENG,D.A.SCOTT,Z.MABEN,O.NUREKI JRNL TITL STRUCTURAL BASIS FOR TARGET DNA CLEAVAGE AND GUIDE RNA JRNL TITL 2 PROCESSING BY CRISPR-CAS LAMBDA 2. JRNL REF COMMUN BIOL V. 8 876 2025 JRNL REFN ESSN 2399-3642 JRNL PMID 40473912 JRNL DOI 10.1038/S42003-025-08300-8 REMARK 2 REMARK 2 RESOLUTION. 2.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.930 REMARK 3 NUMBER OF PARTICLES : 97017 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9IZR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1300050058. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : CASLAMBDA2-CRRNA-TARGET DNA REMARK 245 TERNARY COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.60 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1600.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -9 REMARK 465 GLY A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 GLY A -1 REMARK 465 GLY A 0 REMARK 465 THR A 739 REMARK 465 GLU A 740 REMARK 465 LYS A 741 REMARK 465 G B -38 REMARK 465 G B -37 REMARK 465 G B 17 REMARK 465 G B 18 REMARK 465 C B 19 REMARK 465 DG C 3 REMARK 465 DA C 4 REMARK 465 DT C 5 REMARK 465 DG C 6 REMARK 465 DA C 7 REMARK 465 DG C 8 REMARK 465 DG C 9 REMARK 465 DT C 10 REMARK 465 DG C 11 REMARK 465 DC C 12 REMARK 465 DG C 13 REMARK 465 DC C 14 REMARK 465 DG C 15 REMARK 465 DT C 16 REMARK 465 DG C 17 REMARK 465 GS C 18 REMARK 465 SC C 19 REMARK 465 AS C 20 REMARK 465 SC C 21 REMARK 465 SC C 22 REMARK 465 AS C 23 REMARK 465 PST C 24 REMARK 465 SC C 25 REMARK 465 AS C 26 REMARK 465 PST C 27 REMARK 465 AS C 28 REMARK 465 PST C 29 REMARK 465 AS D -9 REMARK 465 PST D -8 REMARK 465 AS D -7 REMARK 465 PST D -6 REMARK 465 GS D -5 REMARK 465 AS D -4 REMARK 465 PST D -3 REMARK 465 GS D -2 REMARK 465 GS D -1 REMARK 465 PST D 0 REMARK 465 GS D 1 REMARK 465 SC D 2 REMARK 465 DC D 3 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HIS A 329 OH TYR A 349 2.06 REMARK 500 ND1 HIS A 673 OD1 ASN A 675 2.16 REMARK 500 OH TYR A 349 OE2 GLU A 383 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS A 380 79.26 53.48 REMARK 500 PRO A 381 72.88 -67.08 REMARK 500 MET A 394 52.97 -92.51 REMARK 500 GLU A 466 -4.56 73.90 REMARK 500 ASP A 563 -117.31 53.01 REMARK 500 ASN A 581 50.82 -92.82 REMARK 500 VAL A 585 -61.05 -95.19 REMARK 500 ASP A 654 -133.17 52.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 802 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 324 OD1 REMARK 620 2 GLU A 526 OE1 104.7 REMARK 620 3 GLU A 526 OE2 97.4 69.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 803 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 324 OD2 REMARK 620 2 ASN A 326 OD1 83.4 REMARK 620 3 ASP A 680 OD1 128.6 77.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 801 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 499 OD1 REMARK 620 2 G B -30 OP1 88.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B -19 O2 REMARK 620 2 A B -16 OP2 137.4 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-61040 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF CASLAMBDA2-CRRNA-TARGET DNA TERNARY COMPLEX IN REMARK 900 THE NTS-CLEAVING STATE DBREF 9IZR A -9 741 PDB 9IZR 9IZR -9 741 DBREF 9IZR B -38 19 PDB 9IZR 9IZR -38 19 DBREF 9IZR C -10 29 PDB 9IZR 9IZR -10 29 DBREF 9IZR D -9 30 PDB 9IZR 9IZR -9 30 SEQRES 1 A 751 MET GLY HIS HIS HIS HIS HIS HIS GLY GLY MET LYS LYS SEQRES 2 A 751 SER ILE LYS PHE LYS VAL LYS GLY ASN CYS PRO ILE THR SEQRES 3 A 751 LYS ASP VAL ILE ASN GLU TYR LYS GLU TYR TYR ASN LYS SEQRES 4 A 751 CYS SER ASP TRP ILE LYS ASN ASN LEU THR SER ILE THR SEQRES 5 A 751 ILE GLY GLU MET ALA LYS PHE LEU GLN GLU THR LEU GLY SEQRES 6 A 751 LYS ASP VAL ALA TYR ILE SER MET GLY LEU SER ASP GLU SEQRES 7 A 751 TRP LYS ASP LYS PRO LEU TYR HIS LEU PHE THR LYS LYS SEQRES 8 A 751 TYR HIS THR ASN ASN ALA ASP ASN LEU LEU TYR TYR TYR SEQRES 9 A 751 ILE LYS GLU LYS ASN LEU ASP GLY TYR LYS GLY ASN THR SEQRES 10 A 751 LEU ASN ILE GLY ASN THR PHE PHE ARG GLN PHE GLY TYR SEQRES 11 A 751 PHE LYS LEU VAL VAL SER ASN TYR ARG THR LYS ILE ARG SEQRES 12 A 751 THR LEU ASN CYS GLU ILE LYS ARG LYS LYS ILE ASP ALA SEQRES 13 A 751 ASP SER THR SER GLU ASP ILE GLU MET GLN THR MET TYR SEQRES 14 A 751 GLU ILE ILE LYS HIS ASN LEU ASN LYS LYS THR ASP TRP SEQRES 15 A 751 ASP GLU PHE ILE SER TYR ILE GLU ASN VAL GLU ASN PRO SEQRES 16 A 751 ASN ILE ASP ASN ILE ASN ARG TYR LYS LEU LEU ARG LYS SEQRES 17 A 751 CYS PHE CYS GLU ASN GLU ASN MET ILE LYS ASN LYS LEU SEQRES 18 A 751 GLU LEU LEU SER ILE GLU GLN LEU LYS ASN PHE GLY GLY SEQRES 19 A 751 CYS ILE MET LYS GLN HIS ILE ASN SER MET THR LEU ILE SEQRES 20 A 751 ILE GLN HIS PHE LYS ILE GLU GLU LYS GLU ASN SER LEU SEQRES 21 A 751 GLY PHE ILE LEU ASN LEU PRO LEU ASN LYS LYS GLN TYR SEQRES 22 A 751 GLN ILE GLU LEU TRP GLY ASN ARG GLN VAL ASN LYS GLY SEQRES 23 A 751 THR LYS GLU ARG ASP ALA PHE LEU ASN THR TYR GLY GLU SEQRES 24 A 751 ASN ILE VAL PHE ILE ILE ASN ASN ASP GLU LEU TYR VAL SEQRES 25 A 751 VAL PHE SER TYR GLU TYR GLU LEU GLU LYS GLU GLU ALA SEQRES 26 A 751 ASN PHE VAL LYS THR VAL GLY LEU ASP VAL ASN PHE LYS SEQRES 27 A 751 HIS ALA PHE PHE VAL THR SER GLU LYS ASP ASN CYS HIS SEQRES 28 A 751 LEU ASP GLY TYR ILE ASN LEU TYR LYS TYR LEU LEU GLU SEQRES 29 A 751 HIS ASP GLU PHE THR ASN LEU LEU THR ASN ASP GLU LYS SEQRES 30 A 751 LYS ASP TYR GLU GLU LEU SER LYS VAL VAL THR PHE CYS SEQRES 31 A 751 PRO PHE GLU ASN GLN LEU LEU PHE ALA ARG TYR ASN LYS SEQRES 32 A 751 MET SER LYS PHE CYS LYS LYS GLU GLN VAL LEU SER LYS SEQRES 33 A 751 LEU LEU TYR ALA LEU GLN LYS GLN LEU LYS ASP GLU ASN SEQRES 34 A 751 ARG THR LYS GLU TYR ILE TYR VAL SER CYS VAL ASN LYS SEQRES 35 A 751 LEU ARG ALA LYS TYR VAL SER TYR PHE ILE LEU LYS GLU SEQRES 36 A 751 LYS TYR TYR GLU LYS GLN LYS GLU TYR ASP ILE GLU MET SEQRES 37 A 751 GLY PHE VAL ASP ASP SER THR GLU SER LYS GLU SER MET SEQRES 38 A 751 ASP LYS ARG ARG THR GLU PHE PRO PHE ARG ASN THR PRO SEQRES 39 A 751 VAL ALA ASN GLU LEU LEU SER LYS LEU ASN ASN VAL GLN SEQRES 40 A 751 GLN ASP ILE ASN GLY CYS LEU LYS ASN ILE ILE ASN TYR SEQRES 41 A 751 ILE TYR LYS ILE PHE GLU GLN ASN GLY TYR LYS ILE VAL SEQRES 42 A 751 ALA LEU GLU ASN LEU GLU ASN SER ASN PHE GLU LYS LYS SEQRES 43 A 751 GLN VAL LEU PRO THR ILE LYS SER LEU LEU LYS TYR HIS SEQRES 44 A 751 LYS LEU GLU ASN GLN ASN VAL ASN ASP ILE LYS ALA SER SEQRES 45 A 751 ASP LYS VAL LYS GLU TYR ILE GLU ASN GLY TYR TYR GLU SEQRES 46 A 751 LEU ILE THR ASN GLU ASN ASN GLU ILE VAL ASP ALA LYS SEQRES 47 A 751 TYR THR GLU LYS GLY ALA MET LYS VAL LYS ASN ALA ASN SEQRES 48 A 751 PHE PHE ASN LEU MET MET LYS SER LEU HIS PHE ALA SER SEQRES 49 A 751 VAL LYS ASP GLU PHE VAL LEU LEU SER ASN ASN GLY LYS SEQRES 50 A 751 THR GLN ILE ALA LEU VAL PRO SER GLU PHE THR SER GLN SEQRES 51 A 751 MET ASP SER THR ASP HIS CYS LEU TYR MET LYS LYS ASN SEQRES 52 A 751 ASP LYS GLY LYS LEU VAL LYS ALA ASP LYS LYS GLU VAL SEQRES 53 A 751 ARG THR LYS GLN GLU LYS HIS ILE ASN GLY LEU ASN ALA SEQRES 54 A 751 ASP PHE ASN ALA ALA ASN ASN ILE LYS TYR ILE VAL GLU SEQRES 55 A 751 ASN GLU VAL TRP ARG GLU ILE PHE CYS THR ARG PRO LYS SEQRES 56 A 751 LYS ALA GLU TYR ASN VAL PRO SER LEU ASP THR THR LYS SEQRES 57 A 751 LYS GLY PRO SER ALA ILE LEU HIS MET LEU LYS LYS ILE SEQRES 58 A 751 GLU ALA ILE LYS ILE LEU GLU THR GLU LYS SEQRES 1 B 58 G G C U U G U U G U A U A SEQRES 2 B 58 U A U U C U U U U A U A G SEQRES 3 B 58 G U A U U A A A C A A C G SEQRES 4 B 58 G A G A U G A G G U G C G SEQRES 5 B 58 C G U G G C SEQRES 1 C 40 DT DG DT DC DT DA DT DT DT DA DG DG DA SEQRES 2 C 40 DG DA DT DG DA DG DG DT DG DC DG DC DG SEQRES 3 C 40 DT DG GS SC AS SC SC AS PST SC AS PST AS SEQRES 4 C 40 PST SEQRES 1 D 40 AS PST AS PST GS AS PST GS GS PST GS SC DC SEQRES 2 D 40 DA DC DG DC DG DC DA DC DC DT DC DA DT SEQRES 3 D 40 DC DT DC DC DT DA DA DA DT DA DG DA DC SEQRES 4 D 40 DA HET MG A 801 1 HET MG A 802 1 HET MG A 803 1 HET GS A 804 23 HET SC A 805 19 HET AS A 806 21 HET SC A 807 19 HET SC A 808 19 HET AS A 809 21 HET MG B 101 1 HET MG B 102 1 HET MG B 103 1 HET MG B 104 1 HET MG D 101 1 HETNAM MG MAGNESIUM ION HETNAM GS GUANOSINE-5'-THIO-MONOPHOSPHATE HETNAM SC 2-DEOXY-CYTIDINE-5'-THIOPHOSPHORATE HETNAM AS 2-DEOXY-ADENOSINE -5'-THIO-MONOPHOSPHATE FORMUL 5 MG 8(MG 2+) FORMUL 8 GS C10 H14 N5 O6 P S FORMUL 9 SC 3(C9 H14 N3 O6 P S) FORMUL 10 AS 2(C10 H14 N5 O5 P S) HELIX 1 AA1 THR A 16 ASN A 37 1 22 HELIX 2 AA2 THR A 42 GLY A 55 1 14 HELIX 3 AA3 VAL A 58 MET A 63 1 6 HELIX 4 AA4 PRO A 73 PHE A 78 5 6 HELIX 5 AA5 HIS A 83 ASN A 99 1 17 HELIX 6 AA6 GLY A 111 ARG A 116 1 6 HELIX 7 AA7 GLY A 119 THR A 134 1 16 HELIX 8 AA8 THR A 149 ASN A 165 1 17 HELIX 9 AA9 LYS A 169 ASN A 181 1 13 HELIX 10 AB1 ASN A 186 CYS A 201 1 16 HELIX 11 AB2 ASN A 203 LEU A 219 1 17 HELIX 12 AB3 LYS A 220 PHE A 222 5 3 HELIX 13 AB4 THR A 277 THR A 286 1 10 HELIX 14 AB5 ASN A 347 GLU A 354 1 8 HELIX 15 AB6 HIS A 355 ASN A 360 1 6 HELIX 16 AB7 THR A 363 LYS A 375 1 13 HELIX 17 AB8 GLU A 383 PHE A 388 1 6 HELIX 18 AB9 PHE A 397 GLU A 418 1 22 HELIX 19 AC1 ARG A 420 GLY A 459 1 40 HELIX 20 AC2 LYS A 473 PHE A 478 1 6 HELIX 21 AC3 PRO A 479 ASN A 482 5 4 HELIX 22 AC4 THR A 483 ASN A 518 1 36 HELIX 23 AC5 ILE A 542 LEU A 546 5 5 HELIX 24 AC6 LYS A 564 ASN A 571 1 8 HELIX 25 AC7 THR A 590 LEU A 610 1 21 HELIX 26 AC8 HIS A 611 ALA A 613 5 3 HELIX 27 AC9 SER A 614 GLY A 626 1 13 HELIX 28 AD1 ASP A 662 VAL A 666 5 5 HELIX 29 AD2 ASN A 678 ASN A 693 1 16 HELIX 30 AD3 ASN A 693 CYS A 701 1 9 HELIX 31 AD4 GLY A 720 ILE A 731 1 12 SHEET 1 AA1 4 LYS A 2 LYS A 8 0 SHEET 2 AA1 4 LEU A 300 GLU A 307 -1 O VAL A 302 N PHE A 7 SHEET 3 AA1 4 ASN A 290 ILE A 295 -1 N VAL A 292 O VAL A 303 SHEET 4 AA1 4 SER A 233 ILE A 237 -1 N LEU A 236 O ILE A 291 SHEET 1 AA2 3 LYS A 242 GLU A 245 0 SHEET 2 AA2 3 PHE A 252 LEU A 258 -1 O ILE A 253 N GLU A 244 SHEET 3 AA2 3 LYS A 261 LEU A 267 -1 O ILE A 265 N LEU A 254 SHEET 1 AA3 3 THR A 320 VAL A 321 0 SHEET 2 AA3 3 ILE A 522 GLU A 526 1 O ALA A 524 N VAL A 321 SHEET 3 AA3 3 GLN A 629 VAL A 633 1 O VAL A 633 N LEU A 525 SHEET 1 AA4 3 LEU A 323 VAL A 325 0 SHEET 2 AA4 3 PHE A 332 LYS A 337 -1 O VAL A 333 N ASP A 324 SHEET 3 AA4 3 VAL A 376 PHE A 379 -1 O VAL A 377 N GLU A 336 SHEET 1 AA5 3 MET A 641 ASP A 642 0 SHEET 2 AA5 3 CYS A 647 LYS A 652 -1 O CYS A 647 N ASP A 642 SHEET 3 AA5 3 LEU A 658 LYS A 660 -1 O VAL A 659 N LYS A 651 SHEET 1 AA6 3 MET A 641 ASP A 642 0 SHEET 2 AA6 3 CYS A 647 LYS A 652 -1 O CYS A 647 N ASP A 642 SHEET 3 AA6 3 ILE A 734 ILE A 736 1 O LYS A 735 N LEU A 648 LINK O3' GS A 804 P SC A 805 1555 1555 1.57 LINK O3' SC A 805 P AS A 806 1555 1555 1.58 LINK O3' AS A 806 P SC A 807 1555 1555 1.58 LINK O3' SC A 807 P SC A 808 1555 1555 1.58 LINK O3' SC A 808 P AS A 809 1555 1555 1.58 LINK OD1 ASP A 324 MG MG A 802 1555 1555 2.04 LINK OD2 ASP A 324 MG MG A 803 1555 1555 2.06 LINK OD1 ASN A 326 MG MG A 803 1555 1555 2.16 LINK OD1 ASP A 499 MG MG A 801 1555 1555 2.08 LINK OE1 GLU A 526 MG MG A 802 1555 1555 2.08 LINK OE2 GLU A 526 MG MG A 802 1555 1555 1.77 LINK OD1 ASP A 680 MG MG A 803 1555 1555 2.14 LINK OP2 U B -31 MG MG B 103 1555 1555 1.97 LINK OP1 G B -30 MG MG A 801 1555 1555 2.11 LINK O4 U B -23 MG MG B 102 1555 1555 2.25 LINK O2 U B -19 MG MG B 104 1555 1555 2.25 LINK OP2 A B -16 MG MG B 104 1555 1555 2.26 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 TER 6134 GLU A 738 TER 7262 U B 16 TER 7528 DA C 2 TER 8074 DA D 30 HETATM 8075 MG MG A 801 158.037 138.746 159.129 1.00 24.22 MG HETATM 8076 MG MG A 802 132.800 152.656 163.288 1.00 49.08 MG HETATM 8077 MG MG A 803 132.483 152.365 168.322 1.00 50.23 MG HETATM 8078 P GS A 804 129.834 165.914 162.893 1.00 76.13 P HETATM 8079 OP1 GS A 804 129.042 165.850 164.134 1.00 61.88 O HETATM 8080 S2P GS A 804 131.860 166.080 163.451 1.00 83.15 S HETATM 8081 OP3 GS A 804 129.630 167.011 161.894 1.00 69.87 O HETATM 8082 O5' GS A 804 129.739 164.536 162.143 1.00 60.88 O HETATM 8083 C5' GS A 804 128.514 163.781 162.182 1.00 55.81 C HETATM 8084 C4' GS A 804 128.762 162.344 161.796 1.00 52.15 C HETATM 8085 O4' GS A 804 129.390 162.289 160.497 1.00 53.24 O HETATM 8086 C3' GS A 804 129.675 161.558 162.733 1.00 54.02 C HETATM 8087 O3' GS A 804 129.271 160.188 162.735 1.00 53.57 O HETATM 8088 C2' GS A 804 131.037 161.708 162.071 1.00 52.63 C HETATM 8089 C1' GS A 804 130.672 161.693 160.597 1.00 54.34 C HETATM 8090 N9 GS A 804 131.592 162.457 159.741 1.00 53.93 N HETATM 8091 C8 GS A 804 132.028 163.743 159.907 1.00 54.88 C HETATM 8092 N7 GS A 804 132.794 164.157 158.926 1.00 53.82 N HETATM 8093 C5 GS A 804 132.864 163.076 158.066 1.00 52.82 C HETATM 8094 C6 GS A 804 133.537 162.916 156.825 1.00 57.93 C HETATM 8095 O6 GS A 804 134.221 163.751 156.236 1.00 56.68 O HETATM 8096 N1 GS A 804 133.339 161.660 156.286 1.00 62.60 N HETATM 8097 C2 GS A 804 132.584 160.669 156.853 1.00 53.05 C HETATM 8098 N2 GS A 804 132.482 159.522 156.179 1.00 50.38 N HETATM 8099 N3 GS A 804 131.950 160.808 158.013 1.00 48.84 N HETATM 8100 C4 GS A 804 132.129 162.023 158.556 1.00 51.58 C HETATM 8101 N1 SC A 805 134.766 159.272 160.711 1.00 46.46 N HETATM 8102 C2 SC A 805 135.198 159.437 159.392 1.00 44.75 C HETATM 8103 N3 SC A 805 135.652 160.657 159.001 1.00 43.98 N HETATM 8104 C4 SC A 805 135.679 161.684 159.864 1.00 45.70 C HETATM 8105 C5 SC A 805 135.237 161.536 161.211 1.00 43.39 C HETATM 8106 C6 SC A 805 134.789 160.327 161.587 1.00 44.97 C HETATM 8107 O2 SC A 805 135.157 158.474 158.628 1.00 41.46 O HETATM 8108 N4 SC A 805 136.134 162.858 159.429 1.00 47.70 N HETATM 8109 C1' SC A 805 134.334 157.926 161.130 1.00 41.84 C HETATM 8110 C2' SC A 805 134.801 157.537 162.527 1.00 44.04 C HETATM 8111 C3' SC A 805 133.547 157.071 163.264 1.00 43.73 C HETATM 8112 C4' SC A 805 132.503 156.965 162.159 1.00 41.70 C HETATM 8113 O4' SC A 805 132.923 157.907 161.158 1.00 49.21 O HETATM 8114 O3' SC A 805 133.781 155.786 163.840 1.00 54.99 O HETATM 8115 C5' SC A 805 131.095 157.285 162.596 1.00 44.73 C HETATM 8116 O5' SC A 805 131.088 158.578 163.234 1.00 50.72 O HETATM 8117 P SC A 805 129.794 159.213 163.853 1.00 53.12 P HETATM 8118 OP1 SC A 805 128.735 158.055 163.992 1.00 50.25 O HETATM 8119 S2P SC A 805 130.033 160.228 165.440 1.00 50.83 S HETATM 8120 P AS A 806 133.877 155.578 165.403 1.00 48.19 P HETATM 8121 OP1 AS A 806 132.836 154.454 165.770 1.00 45.67 O HETATM 8122 S2P AS A 806 133.558 157.238 166.272 1.00 48.67 S HETATM 8123 O5' AS A 806 135.301 154.955 165.612 1.00 49.50 O HETATM 8124 C5' AS A 806 136.402 155.267 164.732 1.00 54.64 C HETATM 8125 C4' AS A 806 137.629 155.580 165.548 1.00 48.38 C HETATM 8126 O4' AS A 806 138.285 156.737 164.982 1.00 45.51 O HETATM 8127 C3' AS A 806 137.330 155.932 167.004 1.00 57.59 C HETATM 8128 O3' AS A 806 138.374 155.496 167.875 1.00 56.16 O HETATM 8129 C2' AS A 806 137.306 157.451 166.978 1.00 64.55 C HETATM 8130 C1' AS A 806 138.392 157.749 165.966 1.00 59.95 C HETATM 8131 N9 AS A 806 138.264 159.052 165.329 1.00 63.90 N HETATM 8132 C8 AS A 806 137.109 159.662 164.915 1.00 61.77 C HETATM 8133 N7 AS A 806 137.276 160.886 164.481 1.00 67.07 N HETATM 8134 C5 AS A 806 138.640 161.100 164.617 1.00 66.42 C HETATM 8135 C6 AS A 806 139.458 162.214 164.351 1.00 69.54 C HETATM 8136 N6 AS A 806 139.003 163.372 163.865 1.00 69.12 N HETATM 8137 N1 AS A 806 140.777 162.102 164.618 1.00 71.43 N HETATM 8138 C2 AS A 806 141.236 160.952 165.118 1.00 69.26 C HETATM 8139 N3 AS A 806 140.561 159.837 165.409 1.00 66.31 N HETATM 8140 C4 AS A 806 139.261 159.976 165.137 1.00 66.12 C HETATM 8141 N1 SC A 807 139.397 159.977 169.912 1.00 83.32 N HETATM 8142 C2 SC A 807 139.855 160.999 169.075 1.00 83.28 C HETATM 8143 N3 SC A 807 138.947 161.733 168.381 1.00 81.96 N HETATM 8144 C4 SC A 807 137.635 161.487 168.504 1.00 81.50 C HETATM 8145 C5 SC A 807 137.148 160.448 169.350 1.00 83.27 C HETATM 8146 C6 SC A 807 138.054 159.726 170.031 1.00 81.60 C HETATM 8147 O2 SC A 807 141.067 161.204 168.997 1.00 82.38 O HETATM 8148 N4 SC A 807 136.786 162.257 167.822 1.00 83.32 N HETATM 8149 C1' SC A 807 140.408 159.185 170.635 1.00 85.21 C HETATM 8150 C2' SC A 807 140.180 159.062 172.129 1.00 86.87 C HETATM 8151 C3' SC A 807 141.001 157.816 172.428 1.00 79.99 C HETATM 8152 C4' SC A 807 140.746 156.949 171.194 1.00 74.72 C HETATM 8153 O4' SC A 807 140.368 157.861 170.138 1.00 79.36 O HETATM 8154 O3' SC A 807 142.378 158.191 172.442 1.00 85.45 O HETATM 8155 C5' SC A 807 139.676 155.899 171.347 1.00 67.57 C HETATM 8156 O5' SC A 807 139.489 155.248 170.074 1.00 66.49 O HETATM 8157 P SC A 807 138.080 155.164 169.394 1.00 60.85 P HETATM 8158 OP1 SC A 807 137.638 153.655 169.482 1.00 53.79 O HETATM 8159 S2P SC A 807 136.750 156.329 170.090 1.00 64.45 S HETATM 8160 N1 SC A 808 140.230 163.325 172.960 1.00107.96 N HETATM 8161 C2 SC A 808 140.142 164.316 171.977 1.00107.12 C HETATM 8162 N3 SC A 808 139.029 164.368 171.199 1.00100.13 N HETATM 8163 C4 SC A 808 138.037 163.480 171.367 1.00 97.41 C HETATM 8164 C5 SC A 808 138.115 162.453 172.353 1.00 97.49 C HETATM 8165 C6 SC A 808 139.219 162.410 173.117 1.00100.01 C HETATM 8166 O2 SC A 808 141.075 165.110 171.848 1.00110.36 O HETATM 8167 N4 SC A 808 136.955 163.594 170.595 1.00 93.11 N HETATM 8168 C1' SC A 808 141.411 163.335 173.843 1.00110.26 C HETATM 8169 C2' SC A 808 141.358 162.300 174.957 1.00109.27 C HETATM 8170 C3' SC A 808 142.828 161.974 175.156 1.00115.33 C HETATM 8171 C4' SC A 808 143.362 162.032 173.729 1.00109.40 C HETATM 8172 O4' SC A 808 142.554 163.024 173.057 1.00105.44 O HETATM 8173 O3' SC A 808 143.411 163.003 175.957 1.00124.76 O HETATM 8174 C5' SC A 808 143.272 160.730 172.975 1.00104.93 C HETATM 8175 O5' SC A 808 143.834 159.674 173.781 1.00111.72 O HETATM 8176 P SC A 808 143.239 158.223 173.767 1.00106.94 P HETATM 8177 OP1 SC A 808 144.464 157.248 173.588 1.00 77.94 O HETATM 8178 S2P SC A 808 142.103 157.759 175.218 1.00 97.48 S HETATM 8179 P AS A 809 144.945 163.003 176.336 1.00138.96 P HETATM 8180 OP1 AS A 809 145.748 163.651 175.143 1.00122.98 O HETATM 8181 S2P AS A 809 145.468 161.219 176.733 1.00121.04 S HETATM 8182 O5' AS A 809 145.024 164.027 177.522 1.00129.82 O HETATM 8183 C5' AS A 809 145.745 165.273 177.421 1.00123.68 C HETATM 8184 C4' AS A 809 144.789 166.419 177.632 1.00125.09 C HETATM 8185 O4' AS A 809 143.801 166.436 176.585 1.00123.14 O HETATM 8186 C3' AS A 809 143.977 166.351 178.918 1.00125.82 C HETATM 8187 O3' AS A 809 144.698 166.953 179.994 1.00123.33 O HETATM 8188 C2' AS A 809 142.741 167.178 178.574 1.00126.22 C HETATM 8189 C1' AS A 809 142.650 167.127 177.049 1.00126.51 C HETATM 8190 N9 AS A 809 141.464 166.455 176.530 1.00124.71 N HETATM 8191 C8 AS A 809 140.879 165.313 177.009 1.00120.50 C HETATM 8192 N7 AS A 809 139.801 164.949 176.358 1.00120.52 N HETATM 8193 C5 AS A 809 139.665 165.921 175.378 1.00120.42 C HETATM 8194 C6 AS A 809 138.717 166.113 174.355 1.00114.27 C HETATM 8195 N6 AS A 809 137.672 165.304 174.145 1.00109.59 N HETATM 8196 N1 AS A 809 138.873 167.184 173.547 1.00112.42 N HETATM 8197 C2 AS A 809 139.908 168.003 173.757 1.00117.88 C HETATM 8198 N3 AS A 809 140.863 167.924 174.688 1.00122.85 N HETATM 8199 C4 AS A 809 140.684 166.856 175.472 1.00123.75 C HETATM 8200 MG MG B 101 156.433 129.096 154.927 1.00 46.82 MG HETATM 8201 MG MG B 102 166.042 134.142 172.225 1.00 43.06 MG HETATM 8202 MG MG B 103 157.511 132.189 152.241 1.00 15.34 MG HETATM 8203 MG MG B 104 163.012 148.787 172.138 1.00 42.98 MG HETATM 8204 MG MG D 101 134.875 151.263 148.016 1.00 46.13 MG CONECT 2706 8076 CONECT 2707 8077 CONECT 2721 8077 CONECT 4193 8075 CONECT 4416 8076 CONECT 4417 8076 CONECT 5660 8077 CONECT 6240 8202 CONECT 6259 8075 CONECT 6424 8201 CONECT 6501 8203 CONECT 6549 8203 CONECT 8075 4193 6259 CONECT 8076 2706 4416 4417 CONECT 8077 2707 2721 5660 CONECT 8078 8079 8080 8081 8082 CONECT 8079 8078 CONECT 8080 8078 CONECT 8081 8078 CONECT 8082 8078 8083 CONECT 8083 8082 8084 CONECT 8084 8083 8085 8086 CONECT 8085 8084 8089 CONECT 8086 8084 8087 8088 CONECT 8087 8086 8117 CONECT 8088 8086 8089 CONECT 8089 8085 8088 8090 CONECT 8090 8089 8091 8100 CONECT 8091 8090 8092 CONECT 8092 8091 8093 CONECT 8093 8092 8094 8100 CONECT 8094 8093 8095 8096 CONECT 8095 8094 CONECT 8096 8094 8097 CONECT 8097 8096 8098 8099 CONECT 8098 8097 CONECT 8099 8097 8100 CONECT 8100 8090 8093 8099 CONECT 8101 8102 8106 8109 CONECT 8102 8101 8103 8107 CONECT 8103 8102 8104 CONECT 8104 8103 8105 8108 CONECT 8105 8104 8106 CONECT 8106 8101 8105 CONECT 8107 8102 CONECT 8108 8104 CONECT 8109 8101 8110 8113 CONECT 8110 8109 8111 CONECT 8111 8110 8112 8114 CONECT 8112 8111 8113 8115 CONECT 8113 8109 8112 CONECT 8114 8111 8120 CONECT 8115 8112 8116 CONECT 8116 8115 8117 CONECT 8117 8087 8116 8118 8119 CONECT 8118 8117 CONECT 8119 8117 CONECT 8120 8114 8121 8122 8123 CONECT 8121 8120 CONECT 8122 8120 CONECT 8123 8120 8124 CONECT 8124 8123 8125 CONECT 8125 8124 8126 8127 CONECT 8126 8125 8130 CONECT 8127 8125 8128 8129 CONECT 8128 8127 8157 CONECT 8129 8127 8130 CONECT 8130 8126 8129 8131 CONECT 8131 8130 8132 8140 CONECT 8132 8131 8133 CONECT 8133 8132 8134 CONECT 8134 8133 8135 8140 CONECT 8135 8134 8136 8137 CONECT 8136 8135 CONECT 8137 8135 8138 CONECT 8138 8137 8139 CONECT 8139 8138 8140 CONECT 8140 8131 8134 8139 CONECT 8141 8142 8146 8149 CONECT 8142 8141 8143 8147 CONECT 8143 8142 8144 CONECT 8144 8143 8145 8148 CONECT 8145 8144 8146 CONECT 8146 8141 8145 CONECT 8147 8142 CONECT 8148 8144 CONECT 8149 8141 8150 8153 CONECT 8150 8149 8151 CONECT 8151 8150 8152 8154 CONECT 8152 8151 8153 8155 CONECT 8153 8149 8152 CONECT 8154 8151 8176 CONECT 8155 8152 8156 CONECT 8156 8155 8157 CONECT 8157 8128 8156 8158 8159 CONECT 8158 8157 CONECT 8159 8157 CONECT 8160 8161 8165 8168 CONECT 8161 8160 8162 8166 CONECT 8162 8161 8163 CONECT 8163 8162 8164 8167 CONECT 8164 8163 8165 CONECT 8165 8160 8164 CONECT 8166 8161 CONECT 8167 8163 CONECT 8168 8160 8169 8172 CONECT 8169 8168 8170 CONECT 8170 8169 8171 8173 CONECT 8171 8170 8172 8174 CONECT 8172 8168 8171 CONECT 8173 8170 8179 CONECT 8174 8171 8175 CONECT 8175 8174 8176 CONECT 8176 8154 8175 8177 8178 CONECT 8177 8176 CONECT 8178 8176 CONECT 8179 8173 8180 8181 8182 CONECT 8180 8179 CONECT 8181 8179 CONECT 8182 8179 8183 CONECT 8183 8182 8184 CONECT 8184 8183 8185 8186 CONECT 8185 8184 8189 CONECT 8186 8184 8187 8188 CONECT 8187 8186 CONECT 8188 8186 8189 CONECT 8189 8185 8188 8190 CONECT 8190 8189 8191 8199 CONECT 8191 8190 8192 CONECT 8192 8191 8193 CONECT 8193 8192 8194 8199 CONECT 8194 8193 8195 8196 CONECT 8195 8194 CONECT 8196 8194 8197 CONECT 8197 8196 8198 CONECT 8198 8197 8199 CONECT 8199 8190 8193 8198 CONECT 8201 6424 CONECT 8202 6240 CONECT 8203 6501 6549 MASTER 237 0 14 31 19 0 0 6 8200 4 140 71 END