HEADER TRANSFERASE 08-MAR-24 9EMI TITLE KOD-H4 DNA POLYMERASE MUTANT IN A TERNARY COMPLEX CONTAINING SIX HNA TITLE 2 NUCLEOTIDES AND A NON-HYDROLYZABLE TRIPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*CP*A*(XG4))- COMPND 8 3'); COMPND 9 CHAIN: P; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*(6HA)P*(6HA)P*(6HC)P*(6HT)P*(6HG)P*(6HT) COMPND 13 P*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'); COMPND 14 CHAIN: T; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS KOD1; SOURCE 3 ORGANISM_TAXID: 69014; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; 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 KEYWDS POLYMERASE, XNA, MODIFIED NUCLEOTIDES, REVERSE TRANSCRIPTASE, HNA, KEYWDS 2 NON-HYDROLYZABLE TRIPHOSPHATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.GUTFREUND,K.BETZ REVDAT 1 13-NOV-24 9EMI 0 JRNL AUTH C.GUTFREUND,K.BETZ JRNL TITL STRUCTURAL INSIGHTS INTO A DNA POLYMERASE READING THE XENO JRNL TITL 2 NUCLEIC ACID HNA JRNL REF NUCLEIC ACIDS RES. 2024 JRNL REFN ESSN 1362-4962 REMARK 2 REMARK 2 RESOLUTION. 2.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_4788: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.300 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 98883 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.860 REMARK 3 FREE R VALUE TEST SET COUNT : 3816 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 41.0400 - 6.8000 1.00 3807 153 0.1555 0.1359 REMARK 3 2 6.8000 - 5.4000 1.00 3783 150 0.1860 0.2382 REMARK 3 3 5.4000 - 4.7200 1.00 3774 153 0.1648 0.1870 REMARK 3 4 4.7200 - 4.2900 1.00 3787 152 0.1525 0.2202 REMARK 3 5 4.2900 - 3.9800 1.00 3787 153 0.1734 0.2044 REMARK 3 6 3.9800 - 3.7500 0.73 2795 110 0.2042 0.2294 REMARK 3 7 3.7400 - 3.5600 0.65 2454 98 0.2224 0.2415 REMARK 3 8 3.5600 - 3.4000 0.55 2104 90 0.2446 0.2550 REMARK 3 9 3.4000 - 3.2700 1.00 3782 152 0.2436 0.3525 REMARK 3 10 3.2700 - 3.1600 1.00 3824 147 0.2653 0.3278 REMARK 3 11 3.1600 - 3.0600 1.00 3749 152 0.2765 0.3253 REMARK 3 12 3.0600 - 2.9700 1.00 3850 156 0.2944 0.3175 REMARK 3 13 2.9700 - 2.8900 1.00 3784 148 0.3177 0.3877 REMARK 3 14 2.8900 - 2.8200 1.00 3769 151 0.3224 0.3484 REMARK 3 15 2.8200 - 2.7600 1.00 3803 156 0.3265 0.3265 REMARK 3 16 2.7600 - 2.7000 1.00 3771 151 0.3243 0.3728 REMARK 3 17 2.7000 - 2.6500 0.38 1442 61 0.3706 0.4083 REMARK 3 18 2.6500 - 2.6000 0.98 3715 147 0.3560 0.4289 REMARK 3 19 2.6000 - 2.5500 1.00 3814 148 0.3729 0.4051 REMARK 3 20 2.5500 - 2.5100 1.00 3760 155 0.3618 0.3405 REMARK 3 21 2.5100 - 2.4700 1.00 3816 154 0.3844 0.4042 REMARK 3 22 2.4700 - 2.4300 1.00 3751 153 0.3916 0.4462 REMARK 3 23 2.4300 - 2.3900 1.00 3809 153 0.4241 0.4115 REMARK 3 24 2.3900 - 2.3600 1.00 3804 151 0.4404 0.4352 REMARK 3 25 2.3600 - 2.3300 1.00 3782 150 0.4447 0.4516 REMARK 3 26 2.3300 - 2.3000 0.99 3761 150 0.4590 0.4680 REMARK 3 27 2.3000 - 2.2700 0.79 2990 122 0.5065 0.5091 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.490 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.003 7055 REMARK 3 ANGLE : 0.641 9627 REMARK 3 CHIRALITY : 0.044 1030 REMARK 3 PLANARITY : 0.004 1128 REMARK 3 DIHEDRAL : 18.695 1128 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -27.8382 21.2684 -16.8289 REMARK 3 T TENSOR REMARK 3 T11: 0.3858 T22: 0.4230 REMARK 3 T33: 0.4716 T12: -0.0421 REMARK 3 T13: -0.0066 T23: -0.0343 REMARK 3 L TENSOR REMARK 3 L11: 1.3166 L22: 1.1104 REMARK 3 L33: 0.7440 L12: -0.0101 REMARK 3 L13: -0.0429 L23: -0.5602 REMARK 3 S TENSOR REMARK 3 S11: 0.0141 S12: -0.0926 S13: -0.2172 REMARK 3 S21: 0.0101 S22: -0.0539 S23: -0.0349 REMARK 3 S31: 0.1131 S32: -0.0401 S33: 0.0365 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 9EMI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1292137165. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976250 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 101092 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.260 REMARK 200 RESOLUTION RANGE LOW (A) : 46.809 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% W/V PEG 8000, 20% V/V ETHYLENE REMARK 280 GLYCOL 0.02 M D-GLUCOSE, 0.02 M D-MANNOSE, 0.02 M D-GALACTOSE, REMARK 280 0.02 M L-FUCOSE, 0.02 M D-XYLOSE, 0.02 M N-ACETYL-D-GLUCOSAMINE , REMARK 280 0.1 M BICINE/TRIZMA BASE PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 55.72700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 75.77400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 55.72700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 75.77400 REMARK 290 SMTRY3 4 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, T 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 TYR A 757 REMARK 465 GLN A 758 REMARK 465 LYS A 759 REMARK 465 THR A 760 REMARK 465 ARG A 761 REMARK 465 GLN A 762 REMARK 465 VAL A 763 REMARK 465 GLY A 764 REMARK 465 LEU A 765 REMARK 465 SER A 766 REMARK 465 ALA A 767 REMARK 465 TRP A 768 REMARK 465 LEU A 769 REMARK 465 LYS A 770 REMARK 465 PRO A 771 REMARK 465 LYS A 772 REMARK 465 GLY A 773 REMARK 465 THR A 774 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 NH1 ARG A 58 OD2 ASP A 92 2.14 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 6HC T 3 C3' - O3' - P ANGL. DEV. = 14.7 DEGREES REMARK 500 6HT T 4 O3' - P - OP1 ANGL. DEV. = 9.4 DEGREES REMARK 500 6HG T 5 C3' - O3' - P ANGL. DEV. = 9.3 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 ARG A 58 -79.43 -109.37 REMARK 500 ASP A 164 -149.95 -152.93 REMARK 500 PHE A 214 -73.70 -147.64 REMARK 500 GLU A 393 86.35 -65.34 REMARK 500 GLN A 436 -65.04 62.12 REMARK 500 ILE A 471 -64.59 -90.05 REMARK 500 CYS A 506 93.32 -162.64 REMARK 500 ASP A 540 -133.00 -91.79 REMARK 500 PRO A 549 104.77 -55.49 REMARK 500 ASP A 598 -154.35 -89.38 REMARK 500 ASP A 633 4.33 -152.10 REMARK 500 PRO A 695 105.20 -56.13 REMARK 500 ARG A 709 110.85 -30.91 REMARK 500 LYS A 735 17.10 -144.16 REMARK 500 GLN A 736 -56.23 -139.29 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 404 OD2 REMARK 620 2 PHE A 405 O 84.5 REMARK 620 3 GLU A 580 OE2 80.9 120.1 REMARK 620 4 XG4 A 803 O1G 113.3 144.6 93.6 REMARK 620 5 HOH A 904 O 63.7 147.6 63.3 55.4 REMARK 620 6 HOH A 905 O 138.5 123.5 59.2 63.0 87.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG P 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 XG4 A 803 O2A REMARK 620 2 HOH A 914 O 74.6 REMARK 620 3 HOH A 926 O 148.1 89.4 REMARK 620 4 DA P 13 O3' 98.9 165.0 89.6 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8S87 RELATED DB: PDB REMARK 900 KOD-H4, APO STRUCTURE REMARK 900 RELATED ID: 8S8T RELATED DB: PDB REMARK 900 KOD-H4, DNA:DNA, BINARY, REMARK 900 RELATED ID: 8S84 RELATED DB: PDB REMARK 900 KOD-H4, DNA:DNA, TERNARY, NON-HYDROLYZABLE TRIPHOSPHATE REMARK 900 RELATED ID: 9EMF RELATED DB: PDB REMARK 900 KOD-H4, BINARY, ONE HNA NUCLEOTIDE REMARK 900 RELATED ID: 9EMH RELATED DB: PDB REMARK 900 KOD-H4, BINARY, TWO HNA NUCLEOTIDES DBREF 9EMI A 1 774 UNP D0VWU9 D0VWU9_THEKO 1 774 DBREF 9EMI P 1 13 PDB 9EMI 9EMI 1 13 DBREF 9EMI T 1 16 PDB 9EMI 9EMI 1 16 SEQADV 9EMI GLN A 93 UNP D0VWU9 VAL 93 CONFLICT SEQADV 9EMI THR A 114 UNP D0VWU9 ILE 114 CONFLICT SEQADV 9EMI ALA A 141 UNP D0VWU9 ASP 141 CONFLICT SEQADV 9EMI ALA A 143 UNP D0VWU9 GLU 143 CONFLICT SEQADV 9EMI HIS A 147 UNP D0VWU9 GLU 147 CONFLICT SEQADV 9EMI LYS A 383 UNP D0VWU9 SER 383 CONFLICT SEQADV 9EMI GLY A 429 UNP D0VWU9 LYS 429 CONFLICT SEQADV 9EMI LEU A 445 UNP D0VWU9 PHE 445 CONFLICT SEQADV 9EMI LEU A 485 UNP D0VWU9 ALA 485 CONFLICT SEQADV 9EMI VAL A 493 UNP D0VWU9 TYR 493 CONFLICT SEQADV 9EMI HIS A 496 UNP D0VWU9 TYR 496 CONFLICT SEQADV 9EMI MET A 497 UNP D0VWU9 TYR 497 CONFLICT SEQADV 9EMI PHE A 499 UNP D0VWU9 TYR 499 CONFLICT SEQADV 9EMI GLU A 500 UNP D0VWU9 ALA 500 CONFLICT SEQADV 9EMI ASN A 501 UNP D0VWU9 ARG 501 CONFLICT SEQADV 9EMI LEU A 521 UNP D0VWU9 ILE 521 CONFLICT SEQADV 9EMI LYS A 584 UNP D0VWU9 GLU 584 CONFLICT SEQADV 9EMI LYS A 664 UNP D0VWU9 GLU 664 CONFLICT SEQADV 9EMI ARG A 726 UNP D0VWU9 LYS 726 CONFLICT SEQADV 9EMI LYS A 735 UNP D0VWU9 ASN 735 CONFLICT SEQRES 1 A 774 MET ILE LEU ASP THR ASP TYR ILE THR GLU ASP GLY LYS SEQRES 2 A 774 PRO VAL ILE ARG ILE PHE LYS LYS GLU ASN GLY GLU PHE SEQRES 3 A 774 LYS ILE GLU TYR ASP ARG THR PHE GLU PRO TYR PHE TYR SEQRES 4 A 774 ALA LEU LEU LYS ASP ASP SER ALA ILE GLU GLU VAL LYS SEQRES 5 A 774 LYS ILE THR ALA GLU ARG HIS GLY THR VAL VAL THR VAL SEQRES 6 A 774 LYS ARG VAL GLU LYS VAL GLN LYS LYS PHE LEU GLY ARG SEQRES 7 A 774 PRO VAL GLU VAL TRP LYS LEU TYR PHE THR HIS PRO GLN SEQRES 8 A 774 ASP GLN PRO ALA ILE ARG ASP LYS ILE ARG GLU HIS PRO SEQRES 9 A 774 ALA VAL ILE ASP ILE TYR GLU TYR ASP THR PRO PHE ALA SEQRES 10 A 774 LYS ARG TYR LEU ILE ASP LYS GLY LEU VAL PRO MET GLU SEQRES 11 A 774 GLY ASP GLU GLU LEU LYS MET LEU ALA PHE ALA ILE ALA SEQRES 12 A 774 THR LEU TYR HIS GLU GLY GLU GLU PHE ALA GLU GLY PRO SEQRES 13 A 774 ILE LEU MET ILE SER TYR ALA ASP GLU GLU GLY ALA ARG SEQRES 14 A 774 VAL ILE THR TRP LYS ASN VAL ASP LEU PRO TYR VAL ASP SEQRES 15 A 774 VAL VAL SER THR GLU ARG GLU MET ILE LYS ARG PHE LEU SEQRES 16 A 774 ARG VAL VAL LYS GLU LYS ASP PRO ASP VAL LEU ILE THR SEQRES 17 A 774 TYR ASN GLY ASP ASN PHE ASP PHE ALA TYR LEU LYS LYS SEQRES 18 A 774 ARG CYS GLU LYS LEU GLY ILE ASN PHE ALA LEU GLY ARG SEQRES 19 A 774 ASP GLY SER GLU PRO LYS ILE GLN ARG MET GLY ASP ARG SEQRES 20 A 774 PHE ALA VAL GLU VAL LYS GLY ARG ILE HIS PHE ASP LEU SEQRES 21 A 774 TYR PRO VAL ILE ARG ARG THR ILE ASN LEU PRO THR TYR SEQRES 22 A 774 THR LEU GLU ALA VAL TYR GLU ALA VAL PHE GLY GLN PRO SEQRES 23 A 774 LYS GLU LYS VAL TYR ALA GLU GLU ILE THR THR ALA TRP SEQRES 24 A 774 GLU THR GLY GLU ASN LEU GLU ARG VAL ALA ARG TYR SER SEQRES 25 A 774 MET GLU ASP ALA LYS VAL THR TYR GLU LEU GLY LYS GLU SEQRES 26 A 774 PHE LEU PRO MET GLU ALA GLN LEU SER ARG LEU ILE GLY SEQRES 27 A 774 GLN SER LEU TRP ASP VAL SER ARG SER SER THR GLY ASN SEQRES 28 A 774 LEU VAL GLU TRP PHE LEU LEU ARG LYS ALA TYR GLU ARG SEQRES 29 A 774 ASN GLU LEU ALA PRO ASN LYS PRO ASP GLU LYS GLU LEU SEQRES 30 A 774 ALA ARG ARG ARG GLN LYS TYR GLU GLY GLY TYR VAL LYS SEQRES 31 A 774 GLU PRO GLU ARG GLY LEU TRP GLU ASN ILE VAL TYR LEU SEQRES 32 A 774 ASP PHE ARG SER LEU TYR PRO SER ILE ILE ILE THR HIS SEQRES 33 A 774 ASN VAL SER PRO ASP THR LEU ASN ARG GLU GLY CYS GLY SEQRES 34 A 774 GLU TYR ASP VAL ALA PRO GLN VAL GLY HIS ARG PHE CYS SEQRES 35 A 774 LYS ASP LEU PRO GLY PHE ILE PRO SER LEU LEU GLY ASP SEQRES 36 A 774 LEU LEU GLU GLU ARG GLN LYS ILE LYS LYS LYS MET LYS SEQRES 37 A 774 ALA THR ILE ASP PRO ILE GLU ARG LYS LEU LEU ASP TYR SEQRES 38 A 774 ARG GLN ARG LEU ILE LYS ILE LEU ALA ASN SER VAL TYR SEQRES 39 A 774 GLY HIS MET GLY PHE GLU ASN ALA ARG TRP TYR CYS LYS SEQRES 40 A 774 GLU CYS ALA GLU SER VAL THR ALA TRP GLY ARG GLU TYR SEQRES 41 A 774 LEU THR MET THR ILE LYS GLU ILE GLU GLU LYS TYR GLY SEQRES 42 A 774 PHE LYS VAL ILE TYR SER ASP THR ASP GLY PHE PHE ALA SEQRES 43 A 774 THR ILE PRO GLY ALA ASP ALA GLU THR VAL LYS LYS LYS SEQRES 44 A 774 ALA MET GLU PHE LEU LYS TYR ILE ASN ALA LYS LEU PRO SEQRES 45 A 774 GLY ALA LEU GLU LEU GLU TYR GLU GLY PHE TYR LYS ARG SEQRES 46 A 774 GLY PHE PHE VAL THR LYS LYS LYS TYR ALA VAL ILE ASP SEQRES 47 A 774 GLU GLU GLY LYS ILE THR THR ARG GLY LEU GLU ILE VAL SEQRES 48 A 774 ARG ARG ASP TRP SER GLU ILE ALA LYS GLU THR GLN ALA SEQRES 49 A 774 ARG VAL LEU GLU ALA LEU LEU LYS ASP GLY ASP VAL GLU SEQRES 50 A 774 LYS ALA VAL ARG ILE VAL LYS GLU VAL THR GLU LYS LEU SEQRES 51 A 774 SER LYS TYR GLU VAL PRO PRO GLU LYS LEU VAL ILE HIS SEQRES 52 A 774 LYS GLN ILE THR ARG ASP LEU LYS ASP TYR LYS ALA THR SEQRES 53 A 774 GLY PRO HIS VAL ALA VAL ALA LYS ARG LEU ALA ALA ARG SEQRES 54 A 774 GLY VAL LYS ILE ARG PRO GLY THR VAL ILE SER TYR ILE SEQRES 55 A 774 VAL LEU LYS GLY SER GLY ARG ILE GLY ASP ARG ALA ILE SEQRES 56 A 774 PRO PHE ASP GLU PHE ASP PRO THR LYS HIS ARG TYR ASP SEQRES 57 A 774 ALA GLU TYR TYR ILE GLU LYS GLN VAL LEU PRO ALA VAL SEQRES 58 A 774 GLU ARG ILE LEU ARG ALA PHE GLY TYR ARG LYS GLU ASP SEQRES 59 A 774 LEU ARG TYR GLN LYS THR ARG GLN VAL GLY LEU SER ALA SEQRES 60 A 774 TRP LEU LYS PRO LYS GLY THR SEQRES 1 P 13 DG DA DC DC DA DC DG DG DC DC DA DC DA SEQRES 1 T 16 6HA 6HA 6HC 6HT 6HG 6HT DG DG DC DC DG DT DG SEQRES 2 T 16 DG DT DC HET 6HA T 1 19 HET 6HA T 2 22 HET 6HC T 3 20 HET 6HT T 4 21 HET 6HG T 5 23 HET 6HT T 6 21 HET EDO A 801 4 HET MG A 802 1 HET XG4 A 803 31 HET EDO P 101 4 HET MG P 102 1 HET EDO T 101 4 HETNAM 6HA 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(ADENIN-9-YL)-6'-O- HETNAM 2 6HA PHOSPHORYL-D-ARABINO-HEXITOL HETNAM 6HC 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(CYTOSIN-1-YL)-6'-O- HETNAM 2 6HC PHOSPHORYL-D-ARABINO-HEXITOL HETNAM 6HT 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(THYMIN-1-YL)-6'-O- HETNAM 2 6HT PHOSPHORYL-D-ARABINO-HEXITOL HETNAM 6HG 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(GUANIN-9-YL)-6'-O- HETNAM 2 6HG PHOSPHORYL-D-ARABINO-HEXITOL HETNAM EDO 1,2-ETHANEDIOL HETNAM MG MAGNESIUM ION HETNAM XG4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 XG4 PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 6HA 2(C11 H16 N5 O6 P) FORMUL 3 6HC C10 H16 N3 O7 P FORMUL 3 6HT 2(C11 H17 N2 O8 P) FORMUL 3 6HG C11 H16 N5 O7 P FORMUL 4 EDO 3(C2 H6 O2) FORMUL 5 MG 2(MG 2+) FORMUL 6 XG4 C10 H17 N6 O12 P3 FORMUL 10 HOH *32(H2 O) HELIX 1 AA1 ALA A 47 LYS A 52 1 6 HELIX 2 AA2 GLN A 91 HIS A 103 1 13 HELIX 3 AA3 PRO A 115 LYS A 124 1 10 HELIX 4 AA4 THR A 186 ASP A 202 1 17 HELIX 5 AA5 PHE A 214 GLY A 227 1 14 HELIX 6 AA6 LEU A 260 ILE A 268 1 9 HELIX 7 AA7 THR A 274 GLY A 284 1 11 HELIX 8 AA8 TYR A 291 GLY A 302 1 12 HELIX 9 AA9 ASN A 304 GLY A 338 1 35 HELIX 10 AB1 SER A 340 SER A 347 1 8 HELIX 11 AB2 SER A 348 ARG A 364 1 17 HELIX 12 AB3 ASP A 373 ARG A 380 1 8 HELIX 13 AB4 SER A 407 HIS A 416 1 10 HELIX 14 AB5 GLY A 447 THR A 470 1 24 HELIX 15 AB6 ASP A 472 MET A 497 1 26 HELIX 16 AB7 CYS A 506 LYS A 531 1 26 HELIX 17 AB8 ASP A 552 LEU A 571 1 20 HELIX 18 AB9 LEU A 608 ARG A 612 5 5 HELIX 19 AC1 SER A 616 GLY A 634 1 19 HELIX 20 AC2 ASP A 635 LYS A 652 1 18 HELIX 21 AC3 PRO A 656 VAL A 661 5 6 HELIX 22 AC4 ASP A 669 TYR A 673 5 5 HELIX 23 AC5 GLY A 677 ARG A 689 1 13 HELIX 24 AC6 ARG A 709 ASP A 712 5 4 HELIX 25 AC7 ASP A 718 PHE A 720 5 3 HELIX 26 AC8 ASP A 728 LYS A 735 1 8 HELIX 27 AC9 GLN A 736 ARG A 746 1 11 HELIX 28 AD1 ALA A 747 GLY A 749 5 3 HELIX 29 AD2 ARG A 751 LEU A 755 5 5 SHEET 1 AA1 3 ILE A 2 GLU A 10 0 SHEET 2 AA1 3 LYS A 13 GLU A 22 -1 O LYS A 13 N GLU A 10 SHEET 3 AA1 3 GLU A 25 ASP A 31 -1 O LYS A 27 N LYS A 20 SHEET 1 AA2 4 VAL A 68 PHE A 75 0 SHEET 2 AA2 4 ARG A 78 TYR A 86 -1 O VAL A 82 N VAL A 71 SHEET 3 AA2 4 TYR A 37 LEU A 42 -1 N PHE A 38 O LEU A 85 SHEET 4 AA2 4 VAL A 106 TYR A 110 -1 O ILE A 107 N LEU A 41 SHEET 1 AA3 2 ALA A 56 GLU A 57 0 SHEET 2 AA3 2 VAL A 62 VAL A 63 -1 O VAL A 63 N ALA A 56 SHEET 1 AA4 6 VAL A 181 VAL A 183 0 SHEET 2 AA4 6 GLY A 167 THR A 172 1 N THR A 172 O ASP A 182 SHEET 3 AA4 6 ILE A 157 ASP A 164 -1 N TYR A 162 O ARG A 169 SHEET 4 AA4 6 MET A 137 THR A 144 -1 N ALA A 139 O ALA A 163 SHEET 5 AA4 6 VAL A 205 THR A 208 1 O ILE A 207 N PHE A 140 SHEET 6 AA4 6 ILE A 256 ASP A 259 1 O PHE A 258 N THR A 208 SHEET 1 AA5 2 LYS A 240 MET A 244 0 SHEET 2 AA5 2 ARG A 247 GLU A 251 -1 O GLU A 251 N LYS A 240 SHEET 1 AA6 6 LYS A 535 SER A 539 0 SHEET 2 AA6 6 GLY A 543 THR A 547 -1 O PHE A 545 N TYR A 538 SHEET 3 AA6 6 GLY A 395 PHE A 405 -1 N VAL A 401 O ALA A 546 SHEET 4 AA6 6 LEU A 577 THR A 590 -1 O TYR A 583 N ILE A 400 SHEET 5 AA6 6 LYS A 593 ILE A 597 -1 O ILE A 597 N ARG A 585 SHEET 6 AA6 6 ILE A 603 ARG A 606 -1 O ARG A 606 N TYR A 594 SHEET 1 AA7 2 TYR A 431 VAL A 433 0 SHEET 2 AA7 2 ARG A 440 CYS A 442 -1 O PHE A 441 N ASP A 432 SHEET 1 AA8 3 ILE A 662 GLN A 665 0 SHEET 2 AA8 3 VAL A 698 VAL A 703 -1 O TYR A 701 N ILE A 662 SHEET 3 AA8 3 ALA A 714 PRO A 716 -1 O ILE A 715 N ILE A 702 SSBOND 1 CYS A 428 CYS A 442 1555 1555 2.04 SSBOND 2 CYS A 506 CYS A 509 1555 1555 2.04 LINK O3' 6HA T 1 P 6HA T 2 1555 1555 1.56 LINK O3' 6HA T 2 P 6HC T 3 1555 1555 1.56 LINK O3' 6HC T 3 P 6HT T 4 1555 1555 1.56 LINK O3' 6HT T 4 P 6HG T 5 1555 1555 1.56 LINK O3' 6HG T 5 P 6HT T 6 1555 1555 1.56 LINK O3' 6HT T 6 P DG T 7 1555 1555 1.60 LINK OD2 ASP A 404 MG MG A 802 1555 1555 2.70 LINK O PHE A 405 MG MG A 802 1555 1555 3.00 LINK OE2 GLU A 580 MG MG A 802 1555 1555 2.46 LINK MG MG A 802 O1G XG4 A 803 1555 1555 2.82 LINK MG MG A 802 O HOH A 904 1555 1555 2.35 LINK MG MG A 802 O HOH A 905 1555 1555 2.49 LINK O2A XG4 A 803 MG MG P 102 1555 1555 2.18 LINK O HOH A 914 MG MG P 102 1555 1555 2.21 LINK O HOH A 926 MG MG P 102 1555 1555 2.22 LINK O3' DA P 13 MG MG P 102 1555 1555 2.30 CRYST1 111.454 151.548 70.406 90.00 90.00 90.00 P 21 21 2 4 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 0.008972 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006599 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014203 0.00000