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
(ATOM LINES ARE NOT SHOWN.)
END