HEADER HYDROLASE/RNA/DNA 23-JAN-20 6LTU TITLE CRYSTAL STRUCTURE OF CAS12I2 TERNARY COMPLEX WITH DOUBLE MG2+ BOUND IN TITLE 2 CATALYTIC POCKET COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAS12I2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (56-MER); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(*GP*CP*CP*GP*CP*TP*TP*TP*CP*TP*T)-3'); COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA (35-MER); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 5; COMPND 18 MOLECULE: TRANS SSDNA; COMPND 19 CHAIN: E; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 3 ORGANISM_TAXID: 32644; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 4; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630; SOURCE 18 MOL_ID: 5; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 21 ORGANISM_TAXID: 32630 KEYWDS CRISPR-CAS, CAS12I2, CAS12I2 TERNARY COMPLEX, HYDROLASE, HYDROLASE- KEYWDS 2 RNA-DNA COMPLEX, ACTIVE RUVC STATE, WILD TYPE CAS12I2, WT CAS12I2 EXPDTA X-RAY DIFFRACTION AUTHOR X.HUANG,W.SUN,Z.CHENG,M.CHEN,X.LI,J.WANG,G.SHENG,W.GONG,Y.WANG REVDAT 3 29-NOV-23 6LTU 1 REMARK REVDAT 2 04-NOV-20 6LTU 1 JRNL REVDAT 1 28-OCT-20 6LTU 0 JRNL AUTH X.HUANG,W.SUN,Z.CHENG,M.CHEN,X.LI,J.WANG,G.SHENG,W.GONG, JRNL AUTH 2 Y.WANG JRNL TITL STRUCTURAL BASIS FOR TWO METAL-ION CATALYSIS OF DNA CLEAVAGE JRNL TITL 2 BY CAS12I2. JRNL REF NAT COMMUN V. 11 5241 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 33067443 JRNL DOI 10.1038/S41467-020-19072-6 REMARK 2 REMARK 2 RESOLUTION. 2.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 51108 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2504 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 46.8700 - 6.7300 0.98 2895 147 0.1730 0.1934 REMARK 3 2 6.7300 - 5.3400 0.99 2814 160 0.1806 0.1970 REMARK 3 3 5.3400 - 4.6700 0.97 2735 145 0.1599 0.1997 REMARK 3 4 4.6700 - 4.2400 0.96 2693 141 0.1589 0.1745 REMARK 3 5 4.2400 - 3.9400 0.97 2709 133 0.1705 0.2262 REMARK 3 6 3.9400 - 3.7100 0.98 2738 142 0.1993 0.2391 REMARK 3 7 3.7100 - 3.5200 1.00 2770 129 0.2065 0.2252 REMARK 3 8 3.5200 - 3.3700 1.00 2765 133 0.2128 0.2492 REMARK 3 9 3.3700 - 3.2400 1.00 2769 124 0.2176 0.2172 REMARK 3 10 3.2400 - 3.1300 1.00 2798 133 0.2394 0.2683 REMARK 3 11 3.1300 - 3.0300 1.00 2744 160 0.2367 0.2437 REMARK 3 12 3.0300 - 2.9400 1.00 2720 166 0.2436 0.2620 REMARK 3 13 2.9400 - 2.8600 1.00 2731 143 0.2502 0.2754 REMARK 3 14 2.8600 - 2.7900 0.99 2753 140 0.2535 0.2598 REMARK 3 15 2.7900 - 2.7300 0.97 2678 143 0.2577 0.3129 REMARK 3 16 2.7300 - 2.6700 0.93 2524 123 0.2658 0.2892 REMARK 3 17 2.6700 - 2.6200 0.88 2422 126 0.2707 0.3464 REMARK 3 18 2.6200 - 2.5700 0.85 2346 116 0.2672 0.2892 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.298 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.105 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 10785 REMARK 3 ANGLE : 1.062 15008 REMARK 3 CHIRALITY : 0.067 1699 REMARK 3 PLANARITY : 0.006 1574 REMARK 3 DIHEDRAL : 20.781 2202 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6LTU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1300015437. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52840 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.570 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.16000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.98500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6LTR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NACL, 0.1 M TRIS PH 7.2, 18% PEG REMARK 280 6000, EVAPORATION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 140.60900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 140.60900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 47.16450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.78750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 47.16450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.78750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 140.60900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 47.16450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 61.78750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 140.60900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 47.16450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 61.78750 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, C, E 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 220 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 246 LIES ON A SPECIAL POSITION. 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 GLY A 1034 REMARK 465 GLU A 1035 REMARK 465 GLN A 1036 REMARK 465 SER A 1037 REMARK 465 SER A 1038 REMARK 465 ASP A 1039 REMARK 465 GLU A 1040 REMARK 465 GLU A 1041 REMARK 465 ASN A 1042 REMARK 465 PRO A 1043 REMARK 465 ASP A 1044 REMARK 465 GLY A 1045 REMARK 465 SER A 1046 REMARK 465 ARG A 1047 REMARK 465 ILE A 1048 REMARK 465 LYS A 1049 REMARK 465 LEU A 1050 REMARK 465 GLN A 1051 REMARK 465 LEU A 1052 REMARK 465 THR A 1053 REMARK 465 SER A 1054 REMARK 465 G B -1 REMARK 465 G B 0 REMARK 465 U B 50 REMARK 465 A B 51 REMARK 465 A B 52 REMARK 465 U B 53 REMARK 465 C B 54 REMARK 465 U B 55 REMARK 465 U B 56 REMARK 465 DT D 12 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 246 CG CD CE NZ REMARK 470 ASN A 328 CG OD1 ND2 REMARK 470 GLU A 371 CG CD OE1 OE2 REMARK 470 LEU A 384 CG CD1 CD2 REMARK 470 GLN A 409 CG CD OE1 NE2 REMARK 470 PRO A 505 CG CD REMARK 470 VAL A 506 CG1 CG2 REMARK 470 LYS A 678 CG CD CE NZ REMARK 470 LYS A 680 CG CD CE NZ REMARK 470 LYS A 682 CG CD CE NZ REMARK 470 GLU A 683 CG CD OE1 OE2 REMARK 470 TYR A 699 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 776 CG CD CE NZ REMARK 470 GLU A 783 CG CD OE1 OE2 REMARK 470 LYS A 916 CG CD CE NZ REMARK 470 SER A 918 OG REMARK 470 LYS A 924 CG CD CE NZ REMARK 470 ARG A 959 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 960 CG CD CE NZ REMARK 470 SER A 961 OG REMARK 470 TRP A 966 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 966 CZ3 CH2 REMARK 470 LYS A 979 CG CD CE NZ REMARK 470 LYS A1031 CG CD CE NZ REMARK 470 A B 1 P OP1 OP2 REMARK 470 DA E 26 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DA E 26 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA E 26 C2 N3 C4 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 NH2 ARG A 428 OP1 A B 32 2.08 REMARK 500 OD1 ASN A 840 OG1 THR A 843 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 G B 2 C4' - C3' - O3' ANGL. DEV. = -15.6 DEGREES REMARK 500 A B 3 O5' - P - OP1 ANGL. DEV. = -6.7 DEGREES REMARK 500 A B 3 C4' - C3' - O3' ANGL. DEV. = -23.0 DEGREES REMARK 500 A B 47 C4' - C3' - O3' ANGL. DEV. = 13.3 DEGREES REMARK 500 A B 47 C3' - C2' - C1' ANGL. DEV. = 5.8 DEGREES REMARK 500 A B 47 N9 - C1' - C2' ANGL. DEV. = -9.6 DEGREES REMARK 500 A B 47 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 A B 47 C1' - C2' - O2' ANGL. DEV. = -24.7 DEGREES REMARK 500 DC D 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA C 2 C8 - N9 - C1' ANGL. DEV. = 14.2 DEGREES REMARK 500 DA C 2 C4 - N9 - C1' ANGL. DEV. = -14.2 DEGREES REMARK 500 DT C 3 O5' - P - OP2 ANGL. DEV. = -7.8 DEGREES REMARK 500 DG C 15 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES 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 ALA A 158 -123.56 53.56 REMARK 500 ASN A 164 -129.79 52.70 REMARK 500 SER A 166 -19.64 -45.78 REMARK 500 THR A 284 -119.37 -126.44 REMARK 500 TYR A 287 126.08 -37.85 REMARK 500 ILE A 498 -51.13 -128.30 REMARK 500 ILE A 630 -63.94 -93.90 REMARK 500 LYS A 680 -78.01 -107.76 REMARK 500 LYS A 681 -135.96 -110.20 REMARK 500 ASP A 740 -112.44 57.54 REMARK 500 THR A 838 -69.34 -98.43 REMARK 500 LEU A 888 -5.21 71.59 REMARK 500 ASP A 958 -1.61 80.54 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 A1101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 599 OD1 REMARK 620 2 ASP A 599 OD2 49.3 REMARK 620 3 ASN A 601 OD1 103.0 81.4 REMARK 620 4 ASP A1019 OD1 135.9 87.3 73.1 REMARK 620 5 HOH A1253 O 152.7 147.2 70.4 69.0 REMARK 620 6 DC E 24 OP1 72.1 121.4 116.0 150.2 86.8 REMARK 620 7 HOH E 101 O 99.2 110.3 157.3 87.7 91.8 75.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 599 OD1 REMARK 620 2 GLU A 833 OE2 120.1 REMARK 620 3 HOH A1209 O 88.4 77.4 REMARK 620 4 HOH A1242 O 97.7 99.5 173.9 REMARK 620 5 DC E 23 O3' 127.0 109.2 84.2 91.9 REMARK 620 6 DC E 24 OP1 74.1 163.5 95.7 85.9 54.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1221 O REMARK 620 2 HOH A1225 O 96.6 REMARK 620 3 HOH A1415 O 92.4 72.8 REMARK 620 4 HOH B 217 O 103.9 154.6 91.2 REMARK 620 5 HOH B 224 O 98.5 101.1 168.1 90.7 REMARK 620 6 HOH B 245 O 170.0 76.0 79.1 81.7 89.5 REMARK 620 N 1 2 3 4 5 REMARK 999 REMARK 999 SEQUENCE REMARK 999 (1) CHAIN A CONTAINS THE EXPRESSION TAG SER (0). (2) THE AUTHOR REMARK 999 DOES NOT KNOW THE EXACT SEQUENCE OF CHAIN E. THIS SHORT DNA CHAIN REMARK 999 IS THE SUBSTRATE OF CAS12I2 WHICH IS A DNA NUCLEASE AND IT IS BOUND REMARK 999 IN THE CATALYTIC POCKET OF THE PROTEIN. THE AUTHOR BUILT THE MODEL REMARK 999 MANUALLY BASED ON THE FO-FC MAP AND THEN REFINED THE MODEL. DUE TO REMARK 999 THE LIMITED RESOLUTION, THE AUTHOR COULDN'T DISTINGUISH BETWEEN DT REMARK 999 AND DC, DA AND DG. DBREF 6LTU A 0 1054 PDB 6LTU 6LTU 0 1054 DBREF 6LTU B -1 56 PDB 6LTU 6LTU -1 56 DBREF 6LTU D 1 12 PDB 6LTU 6LTU 1 12 DBREF 6LTU C 1 35 PDB 6LTU 6LTU 1 35 DBREF 6LTU E 22 26 PDB 6LTU 6LTU 22 26 SEQRES 1 A 1055 SER MET SER SER ALA ILE LYS SER TYR LYS SER VAL LEU SEQRES 2 A 1055 ARG PRO ASN GLU ARG LYS ASN GLN LEU LEU LYS SER THR SEQRES 3 A 1055 ILE GLN CYS LEU GLU ASP GLY SER ALA PHE PHE PHE LYS SEQRES 4 A 1055 MET LEU GLN GLY LEU PHE GLY GLY ILE THR PRO GLU ILE SEQRES 5 A 1055 VAL ARG PHE SER THR GLU GLN GLU LYS GLN GLN GLN ASP SEQRES 6 A 1055 ILE ALA LEU TRP CYS ALA VAL ASN TRP PHE ARG PRO VAL SEQRES 7 A 1055 SER GLN ASP SER LEU THR HIS THR ILE ALA SER ASP ASN SEQRES 8 A 1055 LEU VAL GLU LYS PHE GLU GLU TYR TYR GLY GLY THR ALA SEQRES 9 A 1055 SER ASP ALA ILE LYS GLN TYR PHE SER ALA SER ILE GLY SEQRES 10 A 1055 GLU SER TYR TYR TRP ASN ASP CYS ARG GLN GLN TYR TYR SEQRES 11 A 1055 ASP LEU CYS ARG GLU LEU GLY VAL GLU VAL SER ASP LEU SEQRES 12 A 1055 THR HIS ASP LEU GLU ILE LEU CYS ARG GLU LYS CYS LEU SEQRES 13 A 1055 ALA VAL ALA THR GLU SER ASN GLN ASN ASN SER ILE ILE SEQRES 14 A 1055 SER VAL LEU PHE GLY THR GLY GLU LYS GLU ASP ARG SER SEQRES 15 A 1055 VAL LYS LEU ARG ILE THR LYS LYS ILE LEU GLU ALA ILE SEQRES 16 A 1055 SER ASN LEU LYS GLU ILE PRO LYS ASN VAL ALA PRO ILE SEQRES 17 A 1055 GLN GLU ILE ILE LEU ASN VAL ALA LYS ALA THR LYS GLU SEQRES 18 A 1055 THR PHE ARG GLN VAL TYR ALA GLY ASN LEU GLY ALA PRO SEQRES 19 A 1055 SER THR LEU GLU LYS PHE ILE ALA LYS ASP GLY GLN LYS SEQRES 20 A 1055 GLU PHE ASP LEU LYS LYS LEU GLN THR ASP LEU LYS LYS SEQRES 21 A 1055 VAL ILE ARG GLY LYS SER LYS GLU ARG ASP TRP CYS CYS SEQRES 22 A 1055 GLN GLU GLU LEU ARG SER TYR VAL GLU GLN ASN THR ILE SEQRES 23 A 1055 GLN TYR ASP LEU TRP ALA TRP GLY GLU MET PHE ASN LYS SEQRES 24 A 1055 ALA HIS THR ALA LEU LYS ILE LYS SER THR ARG ASN TYR SEQRES 25 A 1055 ASN PHE ALA LYS GLN ARG LEU GLU GLN PHE LYS GLU ILE SEQRES 26 A 1055 GLN SER LEU ASN ASN LEU LEU VAL VAL LYS LYS LEU ASN SEQRES 27 A 1055 ASP PHE PHE ASP SER GLU PHE PHE SER GLY GLU GLU THR SEQRES 28 A 1055 TYR THR ILE CYS VAL HIS HIS LEU GLY GLY LYS ASP LEU SEQRES 29 A 1055 SER LYS LEU TYR LYS ALA TRP GLU ASP ASP PRO ALA ASP SEQRES 30 A 1055 PRO GLU ASN ALA ILE VAL VAL LEU CYS ASP ASP LEU LYS SEQRES 31 A 1055 ASN ASN PHE LYS LYS GLU PRO ILE ARG ASN ILE LEU ARG SEQRES 32 A 1055 TYR ILE PHE THR ILE ARG GLN GLU CYS SER ALA GLN ASP SEQRES 33 A 1055 ILE LEU ALA ALA ALA LYS TYR ASN GLN GLN LEU ASP ARG SEQRES 34 A 1055 TYR LYS SER GLN LYS ALA ASN PRO SER VAL LEU GLY ASN SEQRES 35 A 1055 GLN GLY PHE THR TRP THR ASN ALA VAL ILE LEU PRO GLU SEQRES 36 A 1055 LYS ALA GLN ARG ASN ASP ARG PRO ASN SER LEU ASP LEU SEQRES 37 A 1055 ARG ILE TRP LEU TYR LEU LYS LEU ARG HIS PRO ASP GLY SEQRES 38 A 1055 ARG TRP LYS LYS HIS HIS ILE PRO PHE TYR ASP THR ARG SEQRES 39 A 1055 PHE PHE GLN GLU ILE TYR ALA ALA GLY ASN SER PRO VAL SEQRES 40 A 1055 ASP THR CYS GLN PHE ARG THR PRO ARG PHE GLY TYR HIS SEQRES 41 A 1055 LEU PRO LYS LEU THR ASP GLN THR ALA ILE ARG VAL ASN SEQRES 42 A 1055 LYS LYS HIS VAL LYS ALA ALA LYS THR GLU ALA ARG ILE SEQRES 43 A 1055 ARG LEU ALA ILE GLN GLN GLY THR LEU PRO VAL SER ASN SEQRES 44 A 1055 LEU LYS ILE THR GLU ILE SER ALA THR ILE ASN SER LYS SEQRES 45 A 1055 GLY GLN VAL ARG ILE PRO VAL LYS PHE ASP VAL GLY ARG SEQRES 46 A 1055 GLN LYS GLY THR LEU GLN ILE GLY ASP ARG PHE CYS GLY SEQRES 47 A 1055 TYR ASP GLN ASN GLN THR ALA SER HIS ALA TYR SER LEU SEQRES 48 A 1055 TRP GLU VAL VAL LYS GLU GLY GLN TYR HIS LYS GLU LEU SEQRES 49 A 1055 GLY CYS PHE VAL ARG PHE ILE SER SER GLY ASP ILE VAL SEQRES 50 A 1055 SER ILE THR GLU ASN ARG GLY ASN GLN PHE ASP GLN LEU SEQRES 51 A 1055 SER TYR GLU GLY LEU ALA TYR PRO GLN TYR ALA ASP TRP SEQRES 52 A 1055 ARG LYS LYS ALA SER LYS PHE VAL SER LEU TRP GLN ILE SEQRES 53 A 1055 THR LYS LYS ASN LYS LYS LYS GLU ILE VAL THR VAL GLU SEQRES 54 A 1055 ALA LYS GLU LYS PHE ASP ALA ILE CYS LYS TYR GLN PRO SEQRES 55 A 1055 ARG LEU TYR LYS PHE ASN LYS GLU TYR ALA TYR LEU LEU SEQRES 56 A 1055 ARG ASP ILE VAL ARG GLY LYS SER LEU VAL GLU LEU GLN SEQRES 57 A 1055 GLN ILE ARG GLN GLU ILE PHE ARG PHE ILE GLU GLN ASP SEQRES 58 A 1055 CYS GLY VAL THR ARG LEU GLY SER LEU SER LEU SER THR SEQRES 59 A 1055 LEU GLU THR VAL LYS ALA VAL LYS GLY ILE ILE TYR SER SEQRES 60 A 1055 TYR PHE SER THR ALA LEU ASN ALA SER LYS ASN ASN PRO SEQRES 61 A 1055 ILE SER ASP GLU GLN ARG LYS GLU PHE ASP PRO GLU LEU SEQRES 62 A 1055 PHE ALA LEU LEU GLU LYS LEU GLU LEU ILE ARG THR ARG SEQRES 63 A 1055 LYS LYS LYS GLN LYS VAL GLU ARG ILE ALA ASN SER LEU SEQRES 64 A 1055 ILE GLN THR CYS LEU GLU ASN ASN ILE LYS PHE ILE ARG SEQRES 65 A 1055 GLY GLU GLY ASP LEU SER THR THR ASN ASN ALA THR LYS SEQRES 66 A 1055 LYS LYS ALA ASN SER ARG SER MET ASP TRP LEU ALA ARG SEQRES 67 A 1055 GLY VAL PHE ASN LYS ILE ARG GLN LEU ALA PRO MET HIS SEQRES 68 A 1055 ASN ILE THR LEU PHE GLY CYS GLY SER LEU TYR THR SER SEQRES 69 A 1055 HIS GLN ASP PRO LEU VAL HIS ARG ASN PRO ASP LYS ALA SEQRES 70 A 1055 MET LYS CYS ARG TRP ALA ALA ILE PRO VAL LYS ASP ILE SEQRES 71 A 1055 GLY ASP TRP VAL LEU ARG LYS LEU SER GLN ASN LEU ARG SEQRES 72 A 1055 ALA LYS ASN ILE GLY THR GLY GLU TYR TYR HIS GLN GLY SEQRES 73 A 1055 VAL LYS GLU PHE LEU SER HIS TYR GLU LEU GLN ASP LEU SEQRES 74 A 1055 GLU GLU GLU LEU LEU LYS TRP ARG SER ASP ARG LYS SER SEQRES 75 A 1055 ASN ILE PRO CYS TRP VAL LEU GLN ASN ARG LEU ALA GLU SEQRES 76 A 1055 LYS LEU GLY ASN LYS GLU ALA VAL VAL TYR ILE PRO VAL SEQRES 77 A 1055 ARG GLY GLY ARG ILE TYR PHE ALA THR HIS LYS VAL ALA SEQRES 78 A 1055 THR GLY ALA VAL SER ILE VAL PHE ASP GLN LYS GLN VAL SEQRES 79 A 1055 TRP VAL CYS ASN ALA ASP HIS VAL ALA ALA ALA ASN ILE SEQRES 80 A 1055 ALA LEU THR VAL LYS GLY ILE GLY GLU GLN SER SER ASP SEQRES 81 A 1055 GLU GLU ASN PRO ASP GLY SER ARG ILE LYS LEU GLN LEU SEQRES 82 A 1055 THR SER SEQRES 1 B 58 G G A G A A A U C C G U C SEQRES 2 B 58 U U U C A U U G A C G G A SEQRES 3 B 58 A C A G A G C A A G C A G SEQRES 4 B 58 G G U G A C A U U A U U U SEQRES 5 B 58 A A U C U U SEQRES 1 D 12 DG DC DC DG DC DT DT DT DC DT DT DT SEQRES 1 C 35 DA DA DT DA DA DT DG DT DC DA DC DC DC SEQRES 2 C 35 DT DG DC DT DT DG DC DT DC DT DG DT DT SEQRES 3 C 35 DG DA DA DA DG DC DG DG DC SEQRES 1 E 5 DA DC DC DT DA HET MG A1101 1 HET MG A1102 1 HET EDO A1103 4 HET MG B 101 1 HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 6 MG 3(MG 2+) FORMUL 8 EDO C2 H6 O2 FORMUL 10 HOH *325(H2 O) HELIX 1 AA1 ASN A 15 GLY A 46 1 32 HELIX 2 AA2 THR A 48 THR A 56 1 9 HELIX 3 AA3 ASP A 64 TRP A 73 1 10 HELIX 4 AA4 ALA A 87 GLY A 100 1 14 HELIX 5 AA5 SER A 104 ALA A 113 1 10 HELIX 6 AA6 CYS A 124 GLY A 136 1 13 HELIX 7 AA7 GLU A 138 GLU A 152 1 15 HELIX 8 AA8 ASN A 165 GLY A 173 1 9 HELIX 9 AA9 ASP A 179 ASN A 196 1 18 HELIX 10 AB1 VAL A 204 LYS A 216 1 13 HELIX 11 AB2 THR A 221 GLY A 228 1 8 HELIX 12 AB3 SER A 234 LYS A 242 1 9 HELIX 13 AB4 ASP A 249 SER A 265 1 17 HELIX 14 AB5 CYS A 272 THR A 284 1 13 HELIX 15 AB6 ASP A 288 LEU A 327 1 40 HELIX 16 AB7 ASN A 329 ASP A 338 1 10 HELIX 17 AB8 PHE A 339 SER A 342 5 4 HELIX 18 AB9 CYS A 354 LYS A 361 5 8 HELIX 19 AC1 ASP A 362 ASP A 373 1 12 HELIX 20 AC2 ASP A 376 LYS A 389 1 14 HELIX 21 AC3 ILE A 397 ARG A 408 1 12 HELIX 22 AC4 SER A 412 GLN A 432 1 21 HELIX 23 AC5 LEU A 452 ALA A 456 5 5 HELIX 24 AC6 ASP A 491 ILE A 498 1 8 HELIX 25 AC7 THR A 513 GLY A 517 5 5 HELIX 26 AC8 ASN A 532 LYS A 534 5 3 HELIX 27 AC9 HIS A 535 GLN A 551 1 17 HELIX 28 AD1 ALA A 655 GLN A 658 5 4 HELIX 29 AD2 TYR A 659 SER A 671 1 13 HELIX 30 AD3 ALA A 689 TYR A 699 1 11 HELIX 31 AD4 ARG A 702 ARG A 719 1 18 HELIX 32 AD5 SER A 722 GLN A 739 1 18 HELIX 33 AD6 SER A 750 LEU A 772 1 23 HELIX 34 AD7 SER A 781 ASP A 789 1 9 HELIX 35 AD8 ASP A 789 ASN A 825 1 37 HELIX 36 AD9 LYS A 844 LEU A 855 1 12 HELIX 37 AE1 LEU A 855 ALA A 867 1 13 HELIX 38 AE2 PRO A 868 ASN A 871 5 4 HELIX 39 AE3 LYS A 907 ILE A 909 5 3 HELIX 40 AE4 GLY A 910 ARG A 922 1 13 HELIX 41 AE5 THR A 928 TYR A 943 1 16 HELIX 42 AE6 LEU A 945 LYS A 954 1 10 HELIX 43 AE7 PRO A 964 GLY A 977 1 14 HELIX 44 AE8 ALA A 1018 THR A 1029 1 12 SHEET 1 AA1 4 MET A 1 VAL A 11 0 SHEET 2 AA1 4 GLN A 573 ARG A 584 -1 O VAL A 578 N LYS A 6 SHEET 3 AA1 4 ALA A 566 ILE A 568 -1 N THR A 567 O ARG A 575 SHEET 4 AA1 4 PHE A 444 TRP A 446 -1 N TRP A 446 O ALA A 566 SHEET 1 AA2 2 PHE A 74 VAL A 77 0 SHEET 2 AA2 2 TYR A 120 ASP A 123 -1 O TYR A 120 N VAL A 77 SHEET 1 AA3 2 ARG A 468 ARG A 476 0 SHEET 2 AA3 2 TRP A 482 TYR A 490 -1 O ILE A 487 N LEU A 471 SHEET 1 AA4 2 THR A 508 CYS A 509 0 SHEET 2 AA4 2 VAL A 556 SER A 557 1 O VAL A 556 N CYS A 509 SHEET 1 AA5 6 GLN A 618 HIS A 620 0 SHEET 2 AA5 6 CYS A 625 ASP A 634 -1 O CYS A 625 N HIS A 620 SHEET 3 AA5 6 ALA A 607 VAL A 614 -1 N LEU A 610 O ILE A 630 SHEET 4 AA5 6 ARG A 594 ASP A 599 -1 N PHE A 595 O TRP A 611 SHEET 5 AA5 6 PHE A 829 GLU A 833 1 O PHE A 829 N CYS A 596 SHEET 6 AA5 6 THR A 873 CYS A 877 1 O PHE A 875 N ILE A 830 SHEET 1 AA6 2 ILE A 638 ASN A 641 0 SHEET 2 AA6 2 ASN A 644 ASP A 647 -1 O ASN A 644 N ASN A 641 SHEET 1 AA7 2 GLN A 674 LYS A 677 0 SHEET 2 AA7 2 VAL A 685 GLU A 688 -1 O VAL A 687 N ILE A 675 SHEET 1 AA8 2 TRP A 901 PRO A 905 0 SHEET 2 AA8 2 VAL A 982 PRO A 986 -1 O VAL A 983 N ILE A 904 SHEET 1 AA9 3 ILE A 992 ALA A 995 0 SHEET 2 AA9 3 GLN A1012 ASN A1017 -1 O TRP A1014 N ALA A 995 SHEET 3 AA9 3 VAL A1004 VAL A1007 -1 N VAL A1004 O VAL A1015 LINK OD1 ASP A 599 MG MG A1101 1555 1555 2.88 LINK OD2 ASP A 599 MG MG A1101 1555 1555 2.11 LINK OD1 ASP A 599 MG MG A1102 1555 1555 2.12 LINK OD1 ASN A 601 MG MG A1101 1555 1555 2.24 LINK OE2 GLU A 833 MG MG A1102 1555 1555 2.24 LINK OD1 ASP A1019 MG MG A1101 1555 1555 2.37 LINK MG MG A1101 O HOH A1253 1555 1555 2.32 LINK MG MG A1101 OP1 DC E 24 1555 1555 2.04 LINK MG MG A1101 O HOH E 101 1555 1555 2.15 LINK MG MG A1102 O HOH A1209 1555 1555 2.45 LINK MG MG A1102 O HOH A1242 1555 1555 2.17 LINK MG MG A1102 O3' DC E 23 1555 1555 2.60 LINK MG MG A1102 OP1 DC E 24 1555 1555 2.75 LINK O HOH A1221 MG MG B 101 1555 1555 2.13 LINK O HOH A1225 MG MG B 101 1555 1555 2.12 LINK O HOH A1415 MG MG B 101 1555 1555 2.20 LINK MG MG B 101 O HOH B 217 1555 1555 2.20 LINK MG MG B 101 O HOH B 224 1555 1555 2.07 LINK MG MG B 101 O HOH B 245 1555 1555 2.08 CISPEP 1 ASN A 892 PRO A 893 0 4.47 CRYST1 94.329 123.575 281.218 90.00 90.00 90.00 C 2 2 21 8 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 0.010601 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008092 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003556 0.00000