HEADER TRANSFERASE/DNA 01-OCT-13 4C8N TITLE BINARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS TITLE 2 AQUATICUS WITH THE ARITIFICIAL BASE PAIR DNAM-D5SICS AT THE TITLE 3 POSTINSERTION SITE (SEQUENCE CONTEXT 3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LARGE FRAGMENT OF TAQ DNA POLYMERASE I; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KLENOW FRAGMENT, RESIDUES 293-832; COMPND 5 SYNONYM: TAQ POLYMERASE 1, LARGE FRAGMENT OF TAQ DNA POLYMERASE I; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PRIMER, 5'-D(*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*LHOP)-3'; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: TEMPLATE, 5'- COMPND 14 D(*TP*TP*GP*BMNP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP)-3'; COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGDR11; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS TRANSFERASE-DNA COMPLEX, UNNATURAL BASE PAIR, ARTIFICIAL BASE PAIR, KEYWDS 2 BINARY COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.BETZ,D.A.MALYSHEV,T.LAVERGNE,W.WELTE,K.DIEDERICHS,F.E.ROMESBERG, AUTHOR 2 A.MARX REVDAT 3 23-AUG-17 4C8N 1 REMARK REVDAT 2 25-DEC-13 4C8N 1 JRNL ATOM HETATM REVDAT 1 11-DEC-13 4C8N 0 JRNL AUTH K.BETZ,D.A.MALYSHEV,T.LAVERGNE,W.WELTE,K.DIEDERICHS, JRNL AUTH 2 F.E.ROMESBERG,A.MARX JRNL TITL STRUCTURAL INSIGHTS INTO DNA REPLICATION WITHOUT HYDROGEN JRNL TITL 2 BONDS. JRNL REF J.AM.CHEM.SOC. V. 135 18637 2013 JRNL REFN ISSN 0002-7863 JRNL PMID 24283923 JRNL DOI 10.1021/JA409609J REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 88.620 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 55305 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2772 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 49.0853 - 5.1013 1.00 2808 157 0.1482 0.1665 REMARK 3 2 5.1013 - 4.0497 1.00 2698 140 0.1373 0.1773 REMARK 3 3 4.0497 - 3.5379 1.00 2700 128 0.1592 0.1881 REMARK 3 4 3.5379 - 3.2145 1.00 2670 147 0.1804 0.1886 REMARK 3 5 3.2145 - 2.9842 1.00 2621 146 0.2080 0.2478 REMARK 3 6 2.9842 - 2.8082 1.00 2662 136 0.2193 0.2944 REMARK 3 7 2.8082 - 2.6676 1.00 2609 185 0.2111 0.2620 REMARK 3 8 2.6676 - 2.5515 1.00 2636 129 0.2122 0.2537 REMARK 3 9 2.5515 - 2.4533 1.00 2641 126 0.2082 0.2323 REMARK 3 10 2.4533 - 2.3686 1.00 2653 116 0.2141 0.2738 REMARK 3 11 2.3686 - 2.2946 1.00 2626 136 0.2294 0.2841 REMARK 3 12 2.2946 - 2.2290 1.00 2593 151 0.2409 0.3255 REMARK 3 13 2.2290 - 2.1703 1.00 2605 137 0.2496 0.3066 REMARK 3 14 2.1703 - 2.1173 1.00 2618 135 0.2740 0.3550 REMARK 3 15 2.1173 - 2.0692 1.00 2603 123 0.3030 0.3483 REMARK 3 16 2.0692 - 2.0252 1.00 2632 139 0.3360 0.3897 REMARK 3 17 2.0252 - 1.9847 1.00 2629 132 0.3589 0.3972 REMARK 3 18 1.9847 - 1.9472 1.00 2581 124 0.3654 0.4361 REMARK 3 19 1.9472 - 1.9124 0.98 2578 148 0.3950 0.4387 REMARK 3 20 1.9124 - 1.8800 0.93 2370 137 0.4136 0.4393 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.00 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 4976 REMARK 3 ANGLE : 1.062 6839 REMARK 3 CHIRALITY : 0.039 747 REMARK 3 PLANARITY : 0.005 836 REMARK 3 DIHEDRAL : 17.236 1947 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 4C8N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1290058401. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97793 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : DYNAMICALLY BENDABLE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55373 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 REMARK 200 RESOLUTION RANGE LOW (A) : 49.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2M LITHIUM SULFATE, 2% W/V PEG 1000, REMARK 280 50MM HEPES PH 7.5 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 102.15800 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 102.15800 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 32.80850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.54800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.80850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.54800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 102.15800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.80850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.54800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 102.15800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.80850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.54800 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -72.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 DT C 202 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 DG B 108 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC C 207 O4' - C1' - N1 ANGL. DEV. = 2.4 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 ASP A 381 108.63 -164.69 REMARK 500 THR A 399 -168.71 -113.37 REMARK 500 VAL A 433 -73.19 -119.01 REMARK 500 ILE A 503 -99.13 -112.63 REMARK 500 HIS A 784 -123.92 51.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1833 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1834 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1835 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 1836 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 1216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1112 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4C8J RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM REMARK 900 THERMUS AQUATICUS IN AN OPEN BINARY COMPLEX WITH D5SICS AS REMARK 900 TEMPLATING NUCLEOTIDE REMARK 900 RELATED ID: 4C8K RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM REMARK 900 THERMUS AQUATICUS IN A PARTIALLY CLOSED COMPLEX WITH THE ARTIFICIAL REMARK 900 BASE PAIR D5SICS- DNAMTP REMARK 900 RELATED ID: 4C8L RELATED DB: PDB REMARK 900 BINARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM REMARK 900 THERMUS AQUATICUS WITH THE ARTIFICIAL BASE PAIR DNAM-D5SICS AT THE REMARK 900 POSTINSERTION SITE (SEQUENCE CONTEXT 1) REMARK 900 RELATED ID: 4C8M RELATED DB: PDB REMARK 900 BINARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM REMARK 900 THERMUS AQUATICUS WITH THE ARITIFICIAL BASE PAIR D5SICS-DNAM AT THE REMARK 900 POSTINSERTION SITE (SEQUENCE CONTEXT 2) REMARK 900 RELATED ID: 4C8O RELATED DB: PDB REMARK 900 BINARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM REMARK 900 THERMUS AQUATICUS WITH THE ARITIFICIAL BASE PAIR DNAM-D5SICS AT THE REMARK 900 POSTINSERTION SITE (SEQUENCE CONTEXT 2) REMARK 999 REMARK 999 SEQUENCE REMARK 999 5'-T OF THE TEMPLATE IS NOT RESOLVED IN THE STRUCTURE DBREF 4C8N A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 4C8N B 102 112 PDB 4C8N 4C8N 102 112 DBREF 4C8N C 202 215 PDB 4C8N 4C8N 202 215 SEQRES 1 A 540 ALA LEU GLU GLU ALA PRO TRP PRO PRO PRO GLU GLY ALA SEQRES 2 A 540 PHE VAL GLY PHE VAL LEU SER ARG LYS GLU PRO MET TRP SEQRES 3 A 540 ALA ASP LEU LEU ALA LEU ALA ALA ALA ARG GLY GLY ARG SEQRES 4 A 540 VAL HIS ARG ALA PRO GLU PRO TYR LYS ALA LEU ARG ASP SEQRES 5 A 540 LEU LYS GLU ALA ARG GLY LEU LEU ALA LYS ASP LEU SER SEQRES 6 A 540 VAL LEU ALA LEU ARG GLU GLY LEU GLY LEU PRO PRO GLY SEQRES 7 A 540 ASP ASP PRO MET LEU LEU ALA TYR LEU LEU ASP PRO SER SEQRES 8 A 540 ASN THR THR PRO GLU GLY VAL ALA ARG ARG TYR GLY GLY SEQRES 9 A 540 GLU TRP THR GLU GLU ALA GLY GLU ARG ALA ALA LEU SER SEQRES 10 A 540 GLU ARG LEU PHE ALA ASN LEU TRP GLY ARG LEU GLU GLY SEQRES 11 A 540 GLU GLU ARG LEU LEU TRP LEU TYR ARG GLU VAL GLU ARG SEQRES 12 A 540 PRO LEU SER ALA VAL LEU ALA HIS MET GLU ALA THR GLY SEQRES 13 A 540 VAL ARG LEU ASP VAL ALA TYR LEU ARG ALA LEU SER LEU SEQRES 14 A 540 GLU VAL ALA GLU GLU ILE ALA ARG LEU GLU ALA GLU VAL SEQRES 15 A 540 PHE ARG LEU ALA GLY HIS PRO PHE ASN LEU ASN SER ARG SEQRES 16 A 540 ASP GLN LEU GLU ARG VAL LEU PHE ASP GLU LEU GLY LEU SEQRES 17 A 540 PRO ALA ILE GLY LYS THR GLU LYS THR GLY LYS ARG SER SEQRES 18 A 540 THR SER ALA ALA VAL LEU GLU ALA LEU ARG GLU ALA HIS SEQRES 19 A 540 PRO ILE VAL GLU LYS ILE LEU GLN TYR ARG GLU LEU THR SEQRES 20 A 540 LYS LEU LYS SER THR TYR ILE ASP PRO LEU PRO ASP LEU SEQRES 21 A 540 ILE HIS PRO ARG THR GLY ARG LEU HIS THR ARG PHE ASN SEQRES 22 A 540 GLN THR ALA THR ALA THR GLY ARG LEU SER SER SER ASP SEQRES 23 A 540 PRO ASN LEU GLN ASN ILE PRO VAL ARG THR PRO LEU GLY SEQRES 24 A 540 GLN ARG ILE ARG ARG ALA PHE ILE ALA GLU GLU GLY TRP SEQRES 25 A 540 LEU LEU VAL ALA LEU ASP TYR SER GLN ILE GLU LEU ARG SEQRES 26 A 540 VAL LEU ALA HIS LEU SER GLY ASP GLU ASN LEU ILE ARG SEQRES 27 A 540 VAL PHE GLN GLU GLY ARG ASP ILE HIS THR GLU THR ALA SEQRES 28 A 540 SER TRP MET PHE GLY VAL PRO ARG GLU ALA VAL ASP PRO SEQRES 29 A 540 LEU MET ARG ARG ALA ALA LYS THR ILE ASN PHE GLY VAL SEQRES 30 A 540 LEU TYR GLY MET SER ALA HIS ARG LEU SER GLN GLU LEU SEQRES 31 A 540 ALA ILE PRO TYR GLU GLU ALA GLN ALA PHE ILE GLU ARG SEQRES 32 A 540 TYR PHE GLN SER PHE PRO LYS VAL ARG ALA TRP ILE GLU SEQRES 33 A 540 LYS THR LEU GLU GLU GLY ARG ARG ARG GLY TYR VAL GLU SEQRES 34 A 540 THR LEU PHE GLY ARG ARG ARG TYR VAL PRO ASP LEU GLU SEQRES 35 A 540 ALA ARG VAL LYS SER VAL ARG GLU ALA ALA GLU ARG MET SEQRES 36 A 540 ALA PHE ASN MET PRO VAL GLN GLY THR ALA ALA ASP LEU SEQRES 37 A 540 MET LYS LEU ALA MET VAL LYS LEU PHE PRO ARG LEU GLU SEQRES 38 A 540 GLU MET GLY ALA ARG MET LEU LEU GLN VAL HIS ASP GLU SEQRES 39 A 540 LEU VAL LEU GLU ALA PRO LYS GLU ARG ALA GLU ALA VAL SEQRES 40 A 540 ALA ARG LEU ALA LYS GLU VAL MET GLU GLY VAL TYR PRO SEQRES 41 A 540 LEU ALA VAL PRO LEU GLU VAL GLU VAL GLY ILE GLY GLU SEQRES 42 A 540 ASP TRP LEU SER ALA LYS GLU SEQRES 1 B 11 DA DC DC DA DC DG DG DC DG DC LHO SEQRES 1 C 14 DT DT DG BMN DG DC DG DC DC DG DT DG DG SEQRES 2 C 14 DT HET LHO B 112 39 HET BMN C 205 39 HET SO4 A1833 5 HET SO4 A1834 5 HET SO4 A1835 5 HET PGE A1836 24 HET SO4 B1112 5 HET SO4 C1216 5 HETNAM LHO 2-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 LHO PENTOFURANOSYL)-6-METHYLISOQUINOLINE-1(2H)-THIONE HETNAM BMN (1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)- HETNAM 2 BMN 5-O-PHOSPHONO-D-ERYTHRO-PENTITOL HETNAM SO4 SULFATE ION HETNAM PGE TRIETHYLENE GLYCOL FORMUL 2 LHO C15 H18 N O6 P S FORMUL 3 BMN C16 H19 O7 P FORMUL 4 SO4 5(O4 S 2-) FORMUL 7 PGE C6 H14 O4 FORMUL 10 HOH *203(H2 O) HELIX 1 1 GLU A 315 ALA A 319 5 5 HELIX 2 2 GLU A 337 LEU A 342 1 6 HELIX 3 3 ARG A 343 LEU A 345 5 3 HELIX 4 4 LEU A 352 GLU A 363 1 12 HELIX 5 5 ASP A 372 ASP A 381 1 10 HELIX 6 6 THR A 386 GLY A 395 1 10 HELIX 7 7 GLU A 401 LEU A 420 1 20 HELIX 8 8 GLU A 423 VAL A 433 1 11 HELIX 9 9 VAL A 433 GLY A 448 1 16 HELIX 10 10 ASP A 452 GLY A 479 1 28 HELIX 11 11 SER A 486 ASP A 496 1 11 HELIX 12 12 SER A 515 LEU A 522 1 8 HELIX 13 13 PRO A 527 ILE A 546 1 20 HELIX 14 14 LEU A 549 LEU A 552 5 4 HELIX 15 15 ASN A 580 ILE A 584 5 5 HELIX 16 16 THR A 588 ARG A 596 1 9 HELIX 17 17 GLN A 613 GLY A 624 1 12 HELIX 18 18 ASP A 625 GLU A 634 1 10 HELIX 19 19 ASP A 637 GLY A 648 1 12 HELIX 20 20 PRO A 650 VAL A 654 5 5 HELIX 21 21 ASP A 655 GLY A 672 1 18 HELIX 22 22 SER A 674 LEU A 682 1 9 HELIX 23 23 PRO A 685 PHE A 700 1 16 HELIX 24 24 PHE A 700 GLY A 718 1 19 HELIX 25 25 PRO A 731 GLU A 734 5 4 HELIX 26 26 VAL A 737 MET A 775 1 39 HELIX 27 27 ARG A 795 GLY A 809 1 15 HELIX 28 28 ASP A 826 LYS A 831 1 6 SHEET 1 AA 4 ALA A 297 PRO A 298 0 SHEET 2 AA 4 ARG A 331 ARG A 334 1 O VAL A 332 N ALA A 297 SHEET 3 AA 4 LEU A 321 ARG A 328 -1 O ALA A 326 N HIS A 333 SHEET 4 AA 4 PHE A 306 LEU A 311 -1 O PHE A 306 N ALA A 327 SHEET 1 AB 2 ARG A 450 LEU A 451 0 SHEET 2 AB 2 PHE A 598 ILE A 599 -1 O ILE A 599 N ARG A 450 SHEET 1 AC 2 ARG A 563 ASN A 565 0 SHEET 2 AC 2 SER A 575 SER A 577 -1 O SER A 575 N ASN A 565 SHEET 1 AD 4 ARG A 778 VAL A 783 0 SHEET 2 AD 4 GLU A 786 PRO A 792 -1 O GLU A 786 N VAL A 783 SHEET 3 AD 4 TRP A 604 TYR A 611 -1 O LEU A 605 N ALA A 791 SHEET 4 AD 4 VAL A 819 GLY A 824 -1 O GLU A 820 N ASP A 610 SHEET 1 AE 2 TYR A 719 GLU A 721 0 SHEET 2 AE 2 ARG A 727 TYR A 729 -1 O ARG A 728 N VAL A 720 LINK O3' DC B 111 P LHO B 112 1555 1555 1.61 LINK O3' DG C 204 P BMN C 205 1555 1555 1.60 LINK O3' BMN C 205 P DG C 206 1555 1555 1.61 CISPEP 1 TRP A 299 PRO A 300 0 -3.48 CISPEP 2 ASP A 578 PRO A 579 0 -1.68 SITE 1 AC1 1 ARG A 435 SITE 1 AC2 4 SER A 674 ALA A 675 HIS A 676 TYR A 686 SITE 1 AC3 3 ARG A 393 ARG A 419 HOH A2036 SITE 1 AC4 7 ARG A 331 GLN A 613 HIS A 639 ARG A 659 SITE 2 AC4 7 ARG A 660 LYS A 663 PHE A 667 SITE 1 AC5 3 DC B 106 DC C 209 DC C 210 SITE 1 AC6 4 DC B 103 DC B 104 HOH B2001 HOH B2002 CRYST1 65.617 101.096 204.316 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 0.015240 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009892 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004894 0.00000