HEADER TRANSFERASE/DNA 21-SEP-04 1XI1 TITLE PHI29 DNA POLYMERASE SSDNA COMPLEX, MONOCLINIC CRYSTAL FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(P*TP*TP*TP*TP*T)-3'; COMPND 3 CHAIN: C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA POLYMERASE; COMPND 7 CHAIN: A, B; COMPND 8 SYNONYM: EARLY PROTEIN GP2; COMPND 9 EC: 2.7.7.7; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: BACILLUS PHAGE PHI29; SOURCE 5 ORGANISM_TAXID: 10756; SOURCE 6 GENE: 2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA POLYMERASE, PROTEIN-PRIMED, STRAND DISPLACEMENT, PROCESSIVITY, KEYWDS 2 REPLICATION, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.KAMTEKAR,A.J.BERMAN,J.WANG,J.M.LAZARO,M.DE VEGA,L.BLANCO,M.SALAS, AUTHOR 2 T.A.STEITZ REVDAT 6 14-FEB-24 1XI1 1 REMARK REVDAT 5 20-OCT-21 1XI1 1 REMARK SEQADV LINK REVDAT 4 22-JAN-20 1XI1 1 REMARK REVDAT 3 16-JUN-09 1XI1 1 JRNL REVDAT 2 24-FEB-09 1XI1 1 VERSN REVDAT 1 07-DEC-04 1XI1 0 JRNL AUTH J.WANG,S.KAMTEKAR,A.J.BERMAN,T.A.STEITZ JRNL TITL CORRECTION OF X-RAY INTENSITIES FROM SINGLE CRYSTALS JRNL TITL 2 CONTAINING LATTICE-TRANSLOCATION DEFECTS JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 61 67 2005 JRNL REFN ISSN 0907-4449 JRNL PMID 15608377 JRNL DOI 10.1107/S0907444904026721 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.WANG,S.KAMTEKAR,A.J.BERMAN,T.A.STEITZ REMARK 1 TITL CORRECTION OF X-RAY INTENSITIES FROM SINGLE CRYSTALS REMARK 1 TITL 2 CONTAINING LATTICE TRANSLOCATION DEFECTS REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1729277.750 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 66719 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 SET) : 0.243 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 6490 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 9495 REMARK 3 BIN R VALUE (WORKING SET) : 0.4230 REMARK 3 BIN FREE R VALUE : 0.4560 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 1062 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 9336 REMARK 3 NUCLEIC ACID ATOMS : 120 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 235 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 20.92000 REMARK 3 B22 (A**2) : -12.07000 REMARK 3 B33 (A**2) : -8.85000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 12.30000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.59 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.43 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.69 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.920 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.900 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.310 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.000 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.570 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 49.73 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA_REP.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XI1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000030386. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9760 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66719 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 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) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 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: MIR REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM ACETATE, TRIS-HCL, SALT, REMARK 280 AMMONIUM SULFATE, PEG 8000, PH 7.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 85.28150 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, B 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 1 REMARK 465 DT C 2 REMARK 465 DT D 1 REMARK 465 DT D 2 REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 HIS A 3 REMARK 465 MET A 4 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 HIS B 3 REMARK 465 MET B 4 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 PRO A 87 CD PRO A 87 N -0.249 REMARK 500 PRO A 397 CD PRO A 397 N -0.260 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 PRO A 397 C - N - CD ANGL. DEV. = -12.9 DEGREES REMARK 500 PRO A 518 CA - N - CD ANGL. DEV. = -12.2 DEGREES REMARK 500 PRO B 424 CA - N - CD ANGL. DEV. = -17.6 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 ILE A 32 -36.93 -38.00 REMARK 500 HIS A 35 7.58 -64.37 REMARK 500 ASN A 62 67.84 82.11 REMARK 500 PHE A 65 -60.82 -91.21 REMARK 500 ALA A 83 -28.43 -37.35 REMARK 500 ASP A 84 113.31 -170.75 REMARK 500 LEU A 86 105.71 72.50 REMARK 500 PRO A 127 46.99 -70.89 REMARK 500 HIS A 149 71.40 -118.23 REMARK 500 ASP A 186 58.22 -108.41 REMARK 500 THR A 203 147.33 85.00 REMARK 500 GLU A 239 -28.50 61.82 REMARK 500 GLU A 244 105.31 70.48 REMARK 500 SER A 252 74.16 50.03 REMARK 500 THR A 301 -35.67 -134.15 REMARK 500 ARG A 306 75.89 19.00 REMARK 500 LYS A 311 -159.65 -81.41 REMARK 500 ASN A 313 114.99 -9.38 REMARK 500 ALA A 394 48.31 -92.12 REMARK 500 PRO A 397 -96.39 -67.22 REMARK 500 LYS A 422 -148.41 -107.59 REMARK 500 VAL A 425 -80.05 -78.84 REMARK 500 TYR A 426 88.24 -153.43 REMARK 500 THR A 457 -69.69 60.28 REMARK 500 SER A 487 166.16 177.55 REMARK 500 LYS A 507 138.40 -35.44 REMARK 500 GLU A 508 151.03 -42.13 REMARK 500 THR A 522 -42.50 -130.58 REMARK 500 ALA A 531 -96.74 -31.37 REMARK 500 LYS A 539 41.71 -73.58 REMARK 500 GLU A 540 1.33 -157.39 REMARK 500 PHE A 546 99.74 -65.67 REMARK 500 ARG A 552 137.71 -174.22 REMARK 500 HIS B 35 5.88 -65.05 REMARK 500 VAL B 54 66.58 -68.60 REMARK 500 GLN B 55 81.48 -42.75 REMARK 500 ASN B 62 68.15 80.78 REMARK 500 LYS B 110 -100.08 -108.75 REMARK 500 LYS B 112 10.59 -163.56 REMARK 500 TYR B 148 -6.30 -48.22 REMARK 500 ASP B 186 59.48 -106.88 REMARK 500 THR B 203 150.76 81.80 REMARK 500 PHE B 211 67.91 -119.99 REMARK 500 GLU B 239 -26.57 61.38 REMARK 500 GLU B 244 104.66 68.94 REMARK 500 SER B 260 -0.70 -140.57 REMARK 500 LYS B 305 -136.12 -101.61 REMARK 500 ARG B 306 109.60 -20.76 REMARK 500 ARG B 308 -61.23 -20.08 REMARK 500 LYS B 311 -155.58 -79.87 REMARK 500 REMARK 500 THIS ENTRY HAS 65 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 699 DISTANCE = 5.84 ANGSTROMS 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 576 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 145 OD1 REMARK 620 2 ASP A 145 OD2 45.3 REMARK 620 3 ASP A 169 OD2 166.1 120.8 REMARK 620 4 HOH A 633 O 120.5 110.5 58.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 576 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 145 OD2 REMARK 620 2 TYR B 148 OH 85.3 REMARK 620 3 ASP B 169 OD2 102.7 171.5 REMARK 620 N 1 2 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 576 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 576 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XHX RELATED DB: PDB REMARK 900 PHI29 DNA POLYMERASE, ORTHORHOMBIC CRYSTAL FORM REMARK 900 RELATED ID: 1XHZ RELATED DB: PDB REMARK 900 PHI29 DNA POLYMERASE SSDNA COMPLEX, ORTHORHOMBIC CRYSTAL FORM DBREF 1XI1 A 5 575 UNP P03680 DPOL_BPPH2 5 575 DBREF 1XI1 B 5 575 UNP P03680 DPOL_BPPH2 5 575 DBREF 1XI1 C 1 5 PDB 1XI1 1XI1 1 5 DBREF 1XI1 D 1 5 PDB 1XI1 1XI1 1 5 SEQADV 1XI1 ALA A 12 UNP P03680 ASP 12 ENGINEERED MUTATION SEQADV 1XI1 ALA A 66 UNP P03680 ASP 66 ENGINEERED MUTATION SEQADV 1XI1 ALA B 12 UNP P03680 ASP 12 ENGINEERED MUTATION SEQADV 1XI1 ALA B 66 UNP P03680 ASP 66 ENGINEERED MUTATION SEQRES 1 C 5 DT DT DT DT DT SEQRES 1 D 5 DT DT DT DT DT 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 SEQRES 1 B 575 MET LYS HIS MET PRO ARG LYS MET TYR SER CYS ALA PHE SEQRES 2 B 575 GLU THR THR THR LYS VAL GLU ASP CYS ARG VAL TRP ALA SEQRES 3 B 575 TYR GLY TYR MET ASN ILE GLU ASP HIS SER GLU TYR LYS SEQRES 4 B 575 ILE GLY ASN SER LEU ASP GLU PHE MET ALA TRP VAL LEU SEQRES 5 B 575 LYS VAL GLN ALA ASP LEU TYR PHE HIS ASN LEU LYS PHE SEQRES 6 B 575 ALA GLY ALA PHE ILE ILE ASN TRP LEU GLU ARG ASN GLY SEQRES 7 B 575 PHE LYS TRP SER ALA ASP GLY LEU PRO ASN THR TYR ASN SEQRES 8 B 575 THR ILE ILE SER ARG MET GLY GLN TRP TYR MET ILE ASP SEQRES 9 B 575 ILE CYS LEU GLY TYR LYS GLY LYS ARG LYS ILE HIS THR SEQRES 10 B 575 VAL ILE TYR ASP SER LEU LYS LYS LEU PRO PHE PRO VAL SEQRES 11 B 575 LYS LYS ILE ALA LYS ASP PHE LYS LEU THR VAL LEU LYS SEQRES 12 B 575 GLY ASP ILE ASP TYR HIS LYS GLU ARG PRO VAL GLY TYR SEQRES 13 B 575 LYS ILE THR PRO GLU GLU TYR ALA TYR ILE LYS ASN ASP SEQRES 14 B 575 ILE GLN ILE ILE ALA GLU ALA LEU LEU ILE GLN PHE LYS SEQRES 15 B 575 GLN GLY LEU ASP ARG MET THR ALA GLY SER ASP SER LEU SEQRES 16 B 575 LYS GLY PHE LYS ASP ILE ILE THR THR LYS LYS PHE LYS SEQRES 17 B 575 LYS VAL PHE PRO THR LEU SER LEU GLY LEU ASP LYS GLU SEQRES 18 B 575 VAL ARG TYR ALA TYR ARG GLY GLY PHE THR TRP LEU ASN SEQRES 19 B 575 ASP ARG PHE LYS GLU LYS GLU ILE GLY GLU GLY MET VAL SEQRES 20 B 575 PHE ASP VAL ASN SER LEU TYR PRO ALA GLN MET TYR SER SEQRES 21 B 575 ARG LEU LEU PRO TYR GLY GLU PRO ILE VAL PHE GLU GLY SEQRES 22 B 575 LYS TYR VAL TRP ASP GLU ASP TYR PRO LEU HIS ILE GLN SEQRES 23 B 575 HIS ILE ARG CYS GLU PHE GLU LEU LYS GLU GLY TYR ILE SEQRES 24 B 575 PRO THR ILE GLN ILE LYS ARG SER ARG PHE TYR LYS GLY SEQRES 25 B 575 ASN GLU TYR LEU LYS SER SER GLY GLY GLU ILE ALA ASP SEQRES 26 B 575 LEU TRP LEU SER ASN VAL ASP LEU GLU LEU MET LYS GLU SEQRES 27 B 575 HIS TYR ASP LEU TYR ASN VAL GLU TYR ILE SER GLY LEU SEQRES 28 B 575 LYS PHE LYS ALA THR THR GLY LEU PHE LYS ASP PHE ILE SEQRES 29 B 575 ASP LYS TRP THR TYR ILE LYS THR THR SER GLU GLY ALA SEQRES 30 B 575 ILE LYS GLN LEU ALA LYS LEU MET LEU ASN SER LEU TYR SEQRES 31 B 575 GLY LYS PHE ALA SER ASN PRO ASP VAL THR GLY LYS VAL SEQRES 32 B 575 PRO TYR LEU LYS GLU ASN GLY ALA LEU GLY PHE ARG LEU SEQRES 33 B 575 GLY GLU GLU GLU THR LYS ASP PRO VAL TYR THR PRO MET SEQRES 34 B 575 GLY VAL PHE ILE THR ALA TRP ALA ARG TYR THR THR ILE SEQRES 35 B 575 THR ALA ALA GLN ALA CYS TYR ASP ARG ILE ILE TYR CYS SEQRES 36 B 575 ASP THR ASP SER ILE HIS LEU THR GLY THR GLU ILE PRO SEQRES 37 B 575 ASP VAL ILE LYS ASP ILE VAL ASP PRO LYS LYS LEU GLY SEQRES 38 B 575 TYR TRP ALA HIS GLU SER THR PHE LYS ARG ALA LYS TYR SEQRES 39 B 575 LEU ARG GLN LYS THR TYR ILE GLN ASP ILE TYR MET LYS SEQRES 40 B 575 GLU VAL ASP GLY LYS LEU VAL GLU GLY SER PRO ASP ASP SEQRES 41 B 575 TYR THR ASP ILE LYS PHE SER VAL LYS CYS ALA GLY MET SEQRES 42 B 575 THR ASP LYS ILE LYS LYS GLU VAL THR PHE GLU ASN PHE SEQRES 43 B 575 LYS VAL GLY PHE SER ARG LYS MET LYS PRO LYS PRO VAL SEQRES 44 B 575 GLN VAL PRO GLY GLY VAL VAL LEU VAL ASP ASP THR PHE SEQRES 45 B 575 THR ILE LYS HET MG A 576 1 HET MG B 576 1 HETNAM MG MAGNESIUM ION FORMUL 5 MG 2(MG 2+) FORMUL 7 HOH *235(H2 O) HELIX 1 1 LYS A 18 CYS A 22 5 5 HELIX 2 2 SER A 43 GLN A 55 1 13 HELIX 3 3 ASN A 62 ASN A 77 1 16 HELIX 4 4 LEU A 123 LYS A 125 5 3 HELIX 5 5 PRO A 129 PHE A 137 1 9 HELIX 6 6 THR A 159 GLN A 183 1 25 HELIX 7 7 THR A 189 PHE A 211 1 23 HELIX 8 8 SER A 215 ALA A 225 1 11 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 PRO A 468 VAL A 475 5 8 HELIX 16 16 THR A 534 LYS A 539 1 6 HELIX 17 17 SER B 43 VAL B 54 1 12 HELIX 18 18 ASN B 62 ASN B 77 1 16 HELIX 19 19 LEU B 123 LYS B 125 5 3 HELIX 20 20 PRO B 129 PHE B 137 1 9 HELIX 21 21 THR B 159 GLN B 183 1 25 HELIX 22 22 THR B 189 PHE B 211 1 23 HELIX 23 23 SER B 215 ALA B 225 1 11 HELIX 24 24 ASP B 235 LYS B 238 5 4 HELIX 25 25 SER B 252 ARG B 261 1 10 HELIX 26 26 ASN B 330 HIS B 339 1 10 HELIX 27 27 PHE B 360 THR B 373 1 14 HELIX 28 28 GLU B 375 ALA B 394 1 20 HELIX 29 29 TYR B 426 CYS B 448 1 23 HELIX 30 30 PRO B 468 VAL B 475 5 8 HELIX 31 31 THR B 534 LYS B 539 1 6 SHEET 1 A 8 TYR A 38 GLY A 41 0 SHEET 2 A 8 VAL A 24 ASN A 31 -1 N TYR A 27 O GLY A 41 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 ILE A 93 O TYR A 101 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 LYS A 507 -1 O ASP A 503 N LYS A 490 SHEET 7 B 7 VAL A 514 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 LYS A 507 -1 O ASP A 503 N LYS A 490 SHEET 4 C 4 ASP A 523 LYS A 529 -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 GLU A 291 O TYR A 343 SHEET 4 D 4 ALA A 324 SER A 329 -1 O ALA A 324 N CYS A 290 SHEET 1 E 2 GLN A 303 ILE A 304 0 SHEET 2 E 2 GLU A 314 TYR A 315 -1 O GLU A 314 N ILE A 304 SHEET 1 F 2 LYS A 402 LEU A 406 0 SHEET 2 F 2 LEU A 412 LEU A 416 -1 O GLY A 413 N TYR A 405 SHEET 1 G 2 SER A 551 VAL A 561 0 SHEET 2 G 2 GLY A 564 THR A 573 -1 O GLY A 564 N VAL A 561 SHEET 1 H 8 TYR B 38 GLY B 41 0 SHEET 2 H 8 VAL B 24 ASN B 31 -1 N TYR B 27 O GLY B 41 SHEET 3 H 8 MET B 8 THR B 15 -1 N GLU B 14 O TRP B 25 SHEET 4 H 8 ASP B 57 PHE B 60 1 O TYR B 59 N CYS B 11 SHEET 5 H 8 LYS B 114 ASP B 121 1 O TYR B 120 N LEU B 58 SHEET 6 H 8 TRP B 100 TYR B 109 -1 N GLY B 108 O ILE B 115 SHEET 7 H 8 THR B 89 ILE B 94 -1 N ILE B 93 O TYR B 101 SHEET 8 H 8 LYS B 80 TRP B 81 1 N LYS B 80 O TYR B 90 SHEET 1 I 7 THR B 231 LEU B 233 0 SHEET 2 I 7 ILE B 452 ASP B 456 -1 O CYS B 455 N TRP B 232 SHEET 3 I 7 SER B 459 THR B 463 -1 O HIS B 461 N ILE B 453 SHEET 4 I 7 GLU B 241 VAL B 250 -1 N MET B 246 O LEU B 462 SHEET 5 I 7 TRP B 483 ARG B 496 -1 O ALA B 484 N ASP B 249 SHEET 6 I 7 THR B 499 VAL B 509 -1 O THR B 499 N LEU B 495 SHEET 7 I 7 LYS B 512 GLU B 515 -1 O VAL B 514 N LYS B 507 SHEET 1 J 7 THR B 231 LEU B 233 0 SHEET 2 J 7 ILE B 452 ASP B 456 -1 O CYS B 455 N TRP B 232 SHEET 3 J 7 SER B 459 THR B 463 -1 O HIS B 461 N ILE B 453 SHEET 4 J 7 GLU B 241 VAL B 250 -1 N MET B 246 O LEU B 462 SHEET 5 J 7 TRP B 483 ARG B 496 -1 O ALA B 484 N ASP B 249 SHEET 6 J 7 THR B 499 VAL B 509 -1 O THR B 499 N LEU B 495 SHEET 7 J 7 ASP B 523 CYS B 530 -1 O ASP B 523 N MET B 506 SHEET 1 K 4 LEU B 263 GLU B 272 0 SHEET 2 K 4 TYR B 340 THR B 356 -1 O LYS B 352 N ILE B 269 SHEET 3 K 4 LEU B 283 LEU B 294 -1 N ARG B 289 O GLU B 346 SHEET 4 K 4 ALA B 324 SER B 329 -1 O ALA B 324 N CYS B 290 SHEET 1 L 2 GLN B 303 ILE B 304 0 SHEET 2 L 2 GLU B 314 TYR B 315 -1 O GLU B 314 N ILE B 304 SHEET 1 M 2 LYS B 402 LEU B 406 0 SHEET 2 M 2 LEU B 412 LEU B 416 -1 O GLY B 413 N TYR B 405 SHEET 1 N 2 SER B 551 GLN B 560 0 SHEET 2 N 2 VAL B 565 THR B 573 -1 O ASP B 570 N LYS B 555 LINK OD1 ASP A 145 MG MG A 576 1555 1555 2.98 LINK OD2 ASP A 145 MG MG A 576 1555 1555 2.66 LINK OD2 ASP A 169 MG MG A 576 1555 1555 2.40 LINK MG MG A 576 O HOH A 633 1555 1555 2.72 LINK OD2 ASP B 145 MG MG B 576 1555 1555 3.13 LINK OH TYR B 148 MG MG B 576 1555 1555 2.68 LINK OD2 ASP B 169 MG MG B 576 1555 1555 2.69 SITE 1 AC1 4 ASP A 145 TYR A 148 ASP A 169 HOH A 633 SITE 1 AC2 3 ASP B 145 TYR B 148 ASP B 169 CRYST1 60.557 170.563 68.813 90.00 106.99 90.00 P 1 21 1 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 0.016513 0.000000 0.005045 0.00000 SCALE2 0.000000 0.005863 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015195 0.00000