PDB Short entry for 2PYL HEADER REPLICATION, TRANSFERASE/DNA 16-MAY-07 2PYL TITLE PHI29 DNA POLYMERASE COMPLEXED WITH PRIMER-TEMPLATE DNA AND INCOMING TITLE 2 NUCLEOTIDE SUBSTRATES (TERNARY COMPLEX) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(GACTGCTTAC(2DA))-3'; COMPND 3 CHAIN: X; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(CTGACGAATGTACA)-3'; COMPND 7 CHAIN: Y; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA POLYMERASE; COMPND 11 CHAIN: A; COMPND 12 SYNONYM: EARLY PROTEIN GP2; COMPND 13 EC: 2.7.7.7; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: BACILLUS PHAGE PHI29; SOURCE 7 ORGANISM_TAXID: 10756; SOURCE 8 GENE: 2, GP2; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-DNA COMPLEX, REPLICATION, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.J.BERMAN,S.KAMTEKAR,J.L.GOODMAN,J.M.LAZARO,M.DE VEGA,L.BLANCO, AUTHOR 2 M.SALAS,T.A.STEITZ REVDAT 5 30-AUG-23 2PYL 1 REMARK REVDAT 4 20-OCT-21 2PYL 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2PYL 1 VERSN REVDAT 2 07-AUG-07 2PYL 1 JRNL REVDAT 1 17-JUL-07 2PYL 0 JRNL AUTH A.J.BERMAN,S.KAMTEKAR,J.L.GOODMAN,J.M.LAZARO,M.DE VEGA, JRNL AUTH 2 L.BLANCO,M.SALAS,T.A.STEITZ JRNL TITL STRUCTURES OF PHI29 DNA POLYMERASE COMPLEXED WITH SUBSTRATE: JRNL TITL 2 THE MECHANISM OF TRANSLOCATION IN B-FAMILY POLYMERASES JRNL REF EMBO J. V. 26 3494 2007 JRNL REFN ISSN 0261-4189 JRNL PMID 17611604 JRNL DOI 10.1038/SJ.EMBOJ.7601780 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 33015 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3649 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2006 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 224 REMARK 3 BIN FREE R VALUE : 0.3420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4668 REMARK 3 NUCLEIC ACID ATOMS : 505 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 357 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.41000 REMARK 3 B22 (A**2) : -0.22000 REMARK 3 B33 (A**2) : -0.19000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.319 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.240 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.178 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.470 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5415 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3622 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7403 ; 1.271 ; 2.091 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8843 ; 2.144 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 574 ; 6.637 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 214 ;35.640 ;24.112 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 879 ;14.314 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;16.138 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 789 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5511 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1059 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 885 ; 0.189 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3443 ; 0.212 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2396 ; 0.188 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2585 ; 0.082 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 333 ; 0.151 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 1 ; 0.062 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 25 ; 0.165 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.136 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3753 ; 1.610 ; 4.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1166 ; 0.196 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4612 ; 1.776 ; 6.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3325 ; 1.685 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2790 ; 1.883 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2PYL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000042928. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00003 REMARK 200 MONOCHROMATOR : DOUBLE FLAT SI CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36737 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.16600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.85000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.200 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: COPY C OF 1XHX WITHOUT RESIDUES 359-394 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM CHES, 15-20% PEG 8000, PH 9.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 29.46100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.90650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.09950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 78.90650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.46100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.09950 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: X, Y, A 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 1 REMARK 465 LYS A 2 REMARK 465 HIS A 3 REMARK 465 MET A 4 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 306 NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 306 CD ARG A 306 NE -0.166 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 DG X 1 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DG X 1 C1' - O4' - C4' ANGL. DEV. = -6.7 DEGREES REMARK 500 DG X 1 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA X 2 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 DC X 3 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT X 4 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT X 4 C3' - O3' - P ANGL. DEV. = 9.6 DEGREES REMARK 500 DG X 5 C3' - O3' - P ANGL. DEV. = 9.7 DEGREES REMARK 500 DC X 6 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT X 7 O4' - C4' - C3' ANGL. DEV. = -4.0 DEGREES REMARK 500 DT X 7 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT X 8 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC X 10 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC X 10 C3' - O3' - P ANGL. DEV. = 11.9 DEGREES REMARK 500 DA Y 4 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES REMARK 500 DC Y 5 O4' - C1' - C2' ANGL. DEV. = 3.1 DEGREES REMARK 500 DA Y 6 O5' - P - OP1 ANGL. DEV. = -6.9 DEGREES REMARK 500 DA Y 6 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES REMARK 500 DT Y 7 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA Y 11 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT Y 16 O4' - C1' - N1 ANGL. DEV. = 3.4 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 34 83.67 -160.65 REMARK 500 ASN A 62 69.18 79.97 REMARK 500 LYS A 112 41.75 -96.68 REMARK 500 LYS A 138 63.05 61.54 REMARK 500 THR A 203 139.62 85.72 REMARK 500 SER A 252 75.71 51.51 REMARK 500 VAL A 425 -84.70 -93.93 REMARK 500 TYR A 426 82.96 -161.54 REMARK 500 THR A 457 -66.67 75.24 REMARK 500 LYS A 478 -37.16 -136.09 REMARK 500 ARG A 496 -177.79 -177.05 REMARK 500 VAL A 509 -91.90 -114.14 REMARK 500 ASP A 510 73.65 -107.20 REMARK 500 ASP A 520 73.43 -113.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 20 ASP A 21 126.45 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 A3202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 249 OD2 REMARK 620 2 ASP A 458 OD1 78.3 REMARK 620 3 MG A3203 MG 50.4 56.2 REMARK 620 4 TTP A3204 O1A 100.8 67.4 51.0 REMARK 620 5 TTP A3204 O2B 168.3 111.1 128.4 77.5 REMARK 620 6 TTP A3204 O1G 100.7 149.8 99.6 83.4 67.7 REMARK 620 7 HOH A3274 O 117.8 52.5 108.2 93.4 73.9 141.2 REMARK 620 8 HOH A3523 O 55.9 134.0 92.5 121.1 114.8 55.9 145.3 REMARK 620 9 HOH A3525 O 58.8 103.5 47.5 63.7 111.0 53.9 153.4 58.2 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A3203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 249 OD2 REMARK 620 2 ASP A 458 OD1 92.4 REMARK 620 3 TTP A3204 O1A 129.3 75.9 REMARK 620 4 HOH A3525 O 75.7 137.3 80.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 3202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 3203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TTP A 3204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1006 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PY5 RELATED DB: PDB REMARK 900 PHI29 DNA POLYMERASE COMPLEXED WITH SINGLE-STRANDED DNA REMARK 900 RELATED ID: 2PYJ RELATED DB: PDB REMARK 900 PHI29 DNA POLYMERASE COMPLEXED WITH PRIMER-TEMPLATE SUBSTRATE (POST- REMARK 900 TRANSLOCATED BINARY COMPLEX) REMARK 900 RELATED ID: 2PZS RELATED DB: PDB REMARK 900 PHI29 DNA POLYMERASE COMPLEXED WITH PRIMER-TEMPLATE AND INCOMING REMARK 900 NUCLEOTIDE SUBSTRATES (PRE-TRANSLOCATED TERNARY COMPLEX) DBREF 2PYL A 1 575 UNP P03680 DPOL_BPPH2 1 575 DBREF 2PYL X 1 11 PDB 2PYL 2PYL 1 11 DBREF 2PYL Y 4 17 PDB 2PYL 2PYL 4 17 SEQADV 2PYL ALA A 12 UNP P03680 ASP 12 ENGINEERED MUTATION SEQADV 2PYL ALA A 66 UNP P03680 ASP 66 ENGINEERED MUTATION SEQRES 1 X 11 DG DA DC DT DG DC DT DT DA DC 2DA SEQRES 1 Y 14 DA DC DA DT DG DT DA DA DG DC DA DG DT SEQRES 2 Y 14 DC SEQRES 1 A 575 MET LYS HIS MET PRO ARG LYS MET TYR SER CYS ALA PHE SEQRES 2 A 575 GLU THR THR THR LYS VAL GLU ASP CYS ARG VAL TRP ALA SEQRES 3 A 575 TYR GLY TYR MET ASN ILE GLU ASP HIS SER GLU TYR LYS SEQRES 4 A 575 ILE GLY ASN SER LEU ASP GLU PHE MET ALA TRP VAL LEU SEQRES 5 A 575 LYS VAL GLN ALA ASP LEU TYR PHE HIS ASN LEU LYS PHE SEQRES 6 A 575 ALA GLY ALA PHE ILE ILE ASN TRP LEU GLU ARG ASN GLY SEQRES 7 A 575 PHE LYS TRP SER ALA ASP GLY LEU PRO ASN THR TYR ASN SEQRES 8 A 575 THR ILE ILE SER ARG MET GLY GLN TRP TYR MET ILE ASP SEQRES 9 A 575 ILE CYS LEU GLY TYR LYS GLY LYS ARG LYS ILE HIS THR SEQRES 10 A 575 VAL ILE TYR ASP SER LEU LYS LYS LEU PRO PHE PRO VAL SEQRES 11 A 575 LYS LYS ILE ALA LYS ASP PHE LYS LEU THR VAL LEU LYS SEQRES 12 A 575 GLY ASP ILE ASP TYR HIS LYS GLU ARG PRO VAL GLY TYR SEQRES 13 A 575 LYS ILE THR PRO GLU GLU TYR ALA TYR ILE LYS ASN ASP SEQRES 14 A 575 ILE GLN ILE ILE ALA GLU ALA LEU LEU ILE GLN PHE LYS SEQRES 15 A 575 GLN GLY LEU ASP ARG MET THR ALA GLY SER ASP SER LEU SEQRES 16 A 575 LYS GLY PHE LYS ASP ILE ILE THR THR LYS LYS PHE LYS SEQRES 17 A 575 LYS VAL PHE PRO THR LEU SER LEU GLY LEU ASP LYS GLU SEQRES 18 A 575 VAL ARG TYR ALA TYR ARG GLY GLY PHE THR TRP LEU ASN SEQRES 19 A 575 ASP ARG PHE LYS GLU LYS GLU ILE GLY GLU GLY MET VAL SEQRES 20 A 575 PHE ASP VAL ASN SER LEU TYR PRO ALA GLN MET TYR SER SEQRES 21 A 575 ARG LEU LEU PRO TYR GLY GLU PRO ILE VAL PHE GLU GLY SEQRES 22 A 575 LYS TYR VAL TRP ASP GLU ASP TYR PRO LEU HIS ILE GLN SEQRES 23 A 575 HIS ILE ARG CYS GLU PHE GLU LEU LYS GLU GLY TYR ILE SEQRES 24 A 575 PRO THR ILE GLN ILE LYS ARG SER ARG PHE TYR LYS GLY SEQRES 25 A 575 ASN GLU TYR LEU LYS SER SER GLY GLY GLU ILE ALA ASP SEQRES 26 A 575 LEU TRP LEU SER ASN VAL ASP LEU GLU LEU MET LYS GLU SEQRES 27 A 575 HIS TYR ASP LEU TYR ASN VAL GLU TYR ILE SER GLY LEU SEQRES 28 A 575 LYS PHE LYS ALA THR THR GLY LEU PHE LYS ASP PHE ILE SEQRES 29 A 575 ASP LYS TRP THR TYR ILE LYS THR THR SER GLU GLY ALA SEQRES 30 A 575 ILE LYS GLN LEU ALA LYS LEU MET LEU ASN SER LEU TYR SEQRES 31 A 575 GLY LYS PHE ALA SER ASN PRO ASP VAL THR GLY LYS VAL SEQRES 32 A 575 PRO TYR LEU LYS GLU ASN GLY ALA LEU GLY PHE ARG LEU SEQRES 33 A 575 GLY GLU GLU GLU THR LYS ASP PRO VAL TYR THR PRO MET SEQRES 34 A 575 GLY VAL PHE ILE THR ALA TRP ALA ARG TYR THR THR ILE SEQRES 35 A 575 THR ALA ALA GLN ALA CYS TYR ASP ARG ILE ILE TYR CYS SEQRES 36 A 575 ASP THR ASP SER ILE HIS LEU THR GLY THR GLU ILE PRO SEQRES 37 A 575 ASP VAL ILE LYS ASP ILE VAL ASP PRO LYS LYS LEU GLY SEQRES 38 A 575 TYR TRP ALA HIS GLU SER THR PHE LYS ARG ALA LYS TYR SEQRES 39 A 575 LEU ARG GLN LYS THR TYR ILE GLN ASP ILE TYR MET LYS SEQRES 40 A 575 GLU VAL ASP GLY LYS LEU VAL GLU GLY SER PRO ASP ASP SEQRES 41 A 575 TYR THR ASP ILE LYS PHE SER VAL LYS CYS ALA GLY MET SEQRES 42 A 575 THR ASP LYS ILE LYS LYS GLU VAL THR PHE GLU ASN PHE SEQRES 43 A 575 LYS VAL GLY PHE SER ARG LYS MET LYS PRO LYS PRO VAL SEQRES 44 A 575 GLN VAL PRO GLY GLY VAL VAL LEU VAL ASP ASP THR PHE SEQRES 45 A 575 THR ILE LYS MODRES 2PYL 2DA X 11 DA 2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE HET 2DA X 11 20 HET MG A3202 1 HET MG A3203 1 HET TTP A3204 29 HET EDO A1001 4 HET EDO A1002 4 HET EDO A1003 4 HET EDO A1004 4 HET EDO A1005 4 HET EDO A1006 4 HETNAM 2DA 2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM TTP THYMIDINE-5'-TRIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 2DA C10 H14 N5 O5 P FORMUL 4 MG 2(MG 2+) FORMUL 6 TTP C10 H17 N2 O14 P3 FORMUL 7 EDO 6(C2 H6 O2) FORMUL 13 HOH *357(H2 O) HELIX 1 1 SER A 43 GLN A 55 1 13 HELIX 2 2 ASN A 62 ASN A 77 1 16 HELIX 3 3 LEU A 123 LYS A 125 5 3 HELIX 4 4 PRO A 129 LYS A 138 1 10 HELIX 5 5 THR A 159 LYS A 182 1 24 HELIX 6 6 THR A 189 THR A 203 1 15 HELIX 7 7 THR A 203 PHE A 211 1 9 HELIX 8 8 SER A 215 TYR A 224 1 10 HELIX 9 9 ASP A 235 LYS A 238 5 4 HELIX 10 10 SER A 252 ARG A 261 1 10 HELIX 11 11 ASN A 330 HIS A 339 1 10 HELIX 12 12 PHE A 360 THR A 373 1 14 HELIX 13 13 GLU A 375 ALA A 394 1 20 HELIX 14 14 TYR A 426 CYS A 448 1 23 HELIX 15 15 ILE A 471 VAL A 475 5 5 HELIX 16 16 THR A 534 LYS A 539 1 6 SHEET 1 A 8 ASP A 34 GLY A 41 0 SHEET 2 A 8 VAL A 24 ASN A 31 -1 N ASN A 31 O GLU A 37 SHEET 3 A 8 MET A 8 THR A 15 -1 N GLU A 14 O TRP A 25 SHEET 4 A 8 ASP A 57 PHE A 60 1 O TYR A 59 N CYS A 11 SHEET 5 A 8 LYS A 114 ASP A 121 1 O TYR A 120 N LEU A 58 SHEET 6 A 8 TRP A 100 TYR A 109 -1 N GLY A 108 O ILE A 115 SHEET 7 A 8 THR A 89 ILE A 94 -1 N THR A 89 O CYS A 106 SHEET 8 A 8 LYS A 80 TRP A 81 1 N LYS A 80 O TYR A 90 SHEET 1 B 7 THR A 231 LEU A 233 0 SHEET 2 B 7 ILE A 452 ASP A 456 -1 O CYS A 455 N TRP A 232 SHEET 3 B 7 SER A 459 THR A 463 -1 O HIS A 461 N ILE A 453 SHEET 4 B 7 GLY A 245 VAL A 250 -1 N MET A 246 O LEU A 462 SHEET 5 B 7 TRP A 483 ARG A 496 -1 O ALA A 484 N ASP A 249 SHEET 6 B 7 THR A 499 GLU A 508 -1 O ASP A 503 N LYS A 490 SHEET 7 B 7 LEU A 513 GLU A 515 -1 O VAL A 514 N LYS A 507 SHEET 1 C 4 GLU A 241 ILE A 242 0 SHEET 2 C 4 TRP A 483 ARG A 496 -1 O ALA A 492 N ILE A 242 SHEET 3 C 4 THR A 499 GLU A 508 -1 O ASP A 503 N LYS A 490 SHEET 4 C 4 ASP A 523 CYS A 530 -1 O ASP A 523 N MET A 506 SHEET 1 D 4 LEU A 263 GLU A 272 0 SHEET 2 D 4 TYR A 340 THR A 356 -1 O THR A 356 N LEU A 263 SHEET 3 D 4 LEU A 283 LEU A 294 -1 N HIS A 287 O SER A 349 SHEET 4 D 4 ALA A 324 SER A 329 -1 O LEU A 326 N ILE A 288 SHEET 1 E 2 LYS A 402 LEU A 406 0 SHEET 2 E 2 LEU A 412 LEU A 416 -1 O ARG A 415 N VAL A 403 SHEET 1 F 2 SER A 551 VAL A 561 0 SHEET 2 F 2 GLY A 564 THR A 573 -1 O ASP A 570 N LYS A 555 LINK O3' DC X 10 P 2DA X 11 1555 1555 1.58 LINK OD2 ASP A 249 MG MG A3202 1555 1555 2.76 LINK OD2 ASP A 249 MG MG A3203 1555 1555 2.29 LINK OD1 ASP A 458 MG MG A3202 1555 1555 2.73 LINK OD1 ASP A 458 MG MG A3203 1555 1555 2.51 LINK MG MG A3202 MG MG A3203 1555 1555 2.60 LINK MG MG A3202 O1A TTP A3204 1555 1555 2.49 LINK MG MG A3202 O2B TTP A3204 1555 1555 2.22 LINK MG MG A3202 O1G TTP A3204 1555 1555 2.73 LINK MG MG A3202 O HOH A3274 1555 1555 2.69 LINK MG MG A3202 O HOH A3523 1555 1555 2.53 LINK MG MG A3202 O HOH A3525 1555 1555 2.88 LINK MG MG A3203 O1A TTP A3204 1555 1555 2.19 LINK MG MG A3203 O HOH A3525 1555 1555 2.22 SITE 1 AC1 8 ASP A 249 VAL A 250 ASP A 458 MG A3203 SITE 2 AC1 8 TTP A3204 HOH A3274 HOH A3523 HOH A3525 SITE 1 AC2 5 ASP A 249 ASP A 458 MG A3202 TTP A3204 SITE 2 AC2 5 HOH A3525 SITE 1 AC3 21 LEU A 253 TYR A 254 LYS A 371 LYS A 383 SITE 2 AC3 21 ASN A 387 ASP A 458 MG A3202 MG A3203 SITE 3 AC3 21 HOH A3233 HOH A3235 HOH A3265 HOH A3274 SITE 4 AC3 21 HOH A3300 HOH A3501 HOH A3523 HOH A3524 SITE 5 AC3 21 HOH A3525 HOH A3527 2DA X 11 DA Y 6 SITE 6 AC3 21 DT Y 7 SITE 1 AC4 3 ILE A 158 GLU A 291 EDO A1004 SITE 1 AC5 5 GLN A 257 SER A 260 THR A 440 GLY A 481 SITE 2 AC5 5 HOH A3504 SITE 1 AC6 3 LYS A 80 PRO A 87 ASN A 88 SITE 1 AC7 5 ILE A 40 ASN A 42 ILE A 158 ASN A 344 SITE 2 AC7 5 EDO A1001 SITE 1 AC8 4 TYR A 59 ASP A 186 ARG A 187 MET A 188 SITE 1 AC9 5 LYS A 124 THR A 189 GLY A 191 HOH A3318 SITE 2 AC9 5 DA Y 6 CRYST1 58.922 78.199 157.813 90.00 90.00 90.00 P 21 21 21 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 0.016972 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012788 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006337 0.00000