HEADER DNA-BINDING PROTEIN/DNA 31-OCT-05 2C5R TITLE THE STRUCTURE OF PHAGE PHI29 REPLICATION ORGANIZER PROTEIN P16.7 IN TITLE 2 COMPLEX WITH DOUBLE STRANDED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: EARLY PROTEIN P16.7; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 FRAGMENT: RESIDUES 64-130; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: DSDNA AND SSDNA BINDING PROTEIN; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*TP*CP*CP*AP*CP*CP*GP*GP)-3'; COMPND 9 CHAIN: Y; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 5'-D(*CP*CP*GP*GP*TP*GP*GP*AP)-3'; COMPND 13 CHAIN: Z; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS PHAGE PHI29; SOURCE 3 ORGANISM_TAXID: 10756; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 MOL_ID: 3; SOURCE 9 SYNTHETIC: YES KEYWDS DNA-BINDING PROTEIN-DNA COMPLEX, DNA-BINDING PROTEIN, COMPLEX (DNA- KEYWDS 2 BINDING PROTEIN-DNA) EXPDTA X-RAY DIFFRACTION AUTHOR A.ALBERT,M.JIMENEZ,D.MUNOZ-ESPIN,J.L.ASENSIO,J.A.HERMOSO,M.SALAS, AUTHOR 2 W.J.J.MEIJER REVDAT 6 13-DEC-23 2C5R 1 REMARK REVDAT 5 13-JUL-11 2C5R 1 VERSN REVDAT 4 24-FEB-09 2C5R 1 VERSN REVDAT 3 04-JAN-06 2C5R 1 JRNL REVDAT 2 17-NOV-05 2C5R 1 JRNL REVDAT 1 08-NOV-05 2C5R 0 JRNL AUTH A.ALBERT,D.MUNOZ-ESPIN,M.JIMENEZ,J.L.ASENSIO,J.A.HERMOSO, JRNL AUTH 2 M.SALAS,W.J.J.MEIJER JRNL TITL STRUCTURAL BASIS FOR MEMBRANE ANCHORAGE OF VIRAL PHI 29 DNA JRNL TITL 2 DURING REPLICATION. JRNL REF J.BIOL.CHEM. V. 280 42486 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 16275651 JRNL DOI 10.1074/JBC.C500429200 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 12386 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) : 0.254 REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.200 REMARK 3 FREE R VALUE TEST SET COUNT : 960 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 864 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3150 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.3940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3156 REMARK 3 NUCLEIC ACID ATOMS : 328 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 51 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.67000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : 2.81000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.470 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.418 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 22.380 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3558 ; 0.028 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4874 ; 2.218 ; 2.087 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 372 ; 7.900 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 540 ; 0.146 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2580 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1598 ; 0.279 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 117 ; 0.252 ; 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): 62 ; 0.251 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.477 ; 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): 1890 ; 0.397 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3066 ; 0.707 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1668 ; 1.128 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1808 ; 1.762 ; 4.500 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B C D E F REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 8 A 62 6 REMARK 3 1 B 8 B 62 6 REMARK 3 1 C 8 C 62 6 REMARK 3 1 D 8 D 62 6 REMARK 3 1 E 8 E 62 6 REMARK 3 1 F 8 F 62 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 LOOSE POSITIONAL 1 A (A): 459 ; 0.19 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 B (A): 459 ; 0.21 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 C (A): 459 ; 0.19 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 D (A): 459 ; 0.22 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 E (A): 459 ; 0.21 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 F (A): 459 ; 0.35 ; 5.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 459 ; 1.17 ; 10.00 REMARK 3 LOOSE THERMAL 1 B (A**2): 459 ; 1.20 ; 10.00 REMARK 3 LOOSE THERMAL 1 C (A**2): 459 ; 1.02 ; 10.00 REMARK 3 LOOSE THERMAL 1 D (A**2): 459 ; 1.02 ; 10.00 REMARK 3 LOOSE THERMAL 1 E (A**2): 459 ; 1.18 ; 10.00 REMARK 3 LOOSE THERMAL 1 F (A**2): 459 ; 1.25 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 6 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 69 REMARK 3 RESIDUE RANGE : B 7 B 69 REMARK 3 RESIDUE RANGE : C 7 C 69 REMARK 3 RESIDUE RANGE : D 7 D 69 REMARK 3 RESIDUE RANGE : E 7 E 69 REMARK 3 RESIDUE RANGE : F 7 F 69 REMARK 3 ORIGIN FOR THE GROUP (A): 20.1400 9.7025 14.2285 REMARK 3 T TENSOR REMARK 3 T11: 0.0542 T22: 0.3400 REMARK 3 T33: 0.1975 T12: -0.0566 REMARK 3 T13: 0.1014 T23: -0.0584 REMARK 3 L TENSOR REMARK 3 L11: 2.0447 L22: 4.3077 REMARK 3 L33: 2.7576 L12: -1.2069 REMARK 3 L13: -0.3363 L23: 1.4267 REMARK 3 S TENSOR REMARK 3 S11: -0.2690 S12: -0.1114 S13: -0.0341 REMARK 3 S21: -0.0558 S22: 0.1239 S23: 0.0500 REMARK 3 S31: 0.0022 S32: -0.1843 S33: 0.1451 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : Y 9 Y 16 REMARK 3 RESIDUE RANGE : Z 1 Z 8 REMARK 3 ORIGIN FOR THE GROUP (A): 19.9246 18.0440 -1.5662 REMARK 3 T TENSOR REMARK 3 T11: 1.3280 T22: 0.7389 REMARK 3 T33: 0.7471 T12: 0.1334 REMARK 3 T13: -0.0731 T23: -0.0205 REMARK 3 L TENSOR REMARK 3 L11: 79.1442 L22: 30.5486 REMARK 3 L33: 30.0794 L12: 3.3714 REMARK 3 L13: -8.6290 L23: 0.2633 REMARK 3 S TENSOR REMARK 3 S11: -2.1194 S12: -0.2170 S13: 1.2836 REMARK 3 S21: -0.7267 S22: 1.3863 S23: -1.3732 REMARK 3 S31: -0.9213 S32: 0.0255 S33: 0.7330 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2C5R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1290025645. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 173.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM16 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12368 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2BNK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 32.75250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.68000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.05550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.68000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.75250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.05550 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, Y, Z 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 LYS A 63 REMARK 465 THR A 64 REMARK 465 VAL A 65 REMARK 465 LYS B 63 REMARK 465 THR B 64 REMARK 465 VAL B 65 REMARK 465 LYS C 63 REMARK 465 THR C 64 REMARK 465 VAL C 65 REMARK 465 LYS D 63 REMARK 465 THR D 64 REMARK 465 VAL D 65 REMARK 465 LYS E 63 REMARK 465 THR E 64 REMARK 465 VAL E 65 REMARK 465 LYS F 63 REMARK 465 THR F 64 REMARK 465 VAL F 65 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 129 CA C O CB CG CD CE REMARK 470 LYS A 129 NZ REMARK 470 LYS B 129 CA C O CB CG CD CE REMARK 470 LYS B 129 NZ REMARK 470 LYS C 129 CA C O CB CG CD CE REMARK 470 LYS C 129 NZ REMARK 470 LYS D 129 CA C O CB CG CD CE REMARK 470 LYS D 129 NZ REMARK 470 LYS E 129 CA C O CB CG CD CE REMARK 470 LYS E 129 NZ REMARK 470 LYS F 129 CA C O CB CG CD CE REMARK 470 LYS F 129 NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O SER A 127 N LYS A 129 1.64 REMARK 500 N2 DG Z 6 O HOH Z 2003 2.05 REMARK 500 OE2 GLU F 118 O HOH F 2004 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 SER B 68 CB SER B 68 OG 0.089 REMARK 500 GLU B 71 CG GLU B 71 CD 0.126 REMARK 500 SER D 68 CB SER D 68 OG 0.106 REMARK 500 DC Y 10 C2 DC Y 10 N3 0.049 REMARK 500 DC Y 10 N3 DC Y 10 C4 -0.046 REMARK 500 DC Y 13 C2 DC Y 13 N3 0.049 REMARK 500 DC Y 14 C2 DC Y 14 N3 0.050 REMARK 500 DC Z 1 C2 DC Z 1 N3 0.052 REMARK 500 DC Z 2 C2 DC Z 2 N3 0.056 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 ASP A 88 CB - CG - OD2 ANGL. DEV. = 8.2 DEGREES REMARK 500 LEU A 128 CA - C - O ANGL. DEV. = 27.9 DEGREES REMARK 500 LEU B 67 CA - CB - CG ANGL. DEV. = 16.0 DEGREES REMARK 500 ASP B 92 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 112 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG C 112 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP D 92 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG D 112 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG D 112 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG E 125 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG F 112 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 LEU F 128 O - C - N ANGL. DEV. = -10.8 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 ASN A 95 49.52 -68.77 REMARK 500 GLN A 96 -3.50 -153.22 REMARK 500 ARG A 97 54.15 27.43 REMARK 500 GLU B 91 -61.29 -26.52 REMARK 500 ASN B 95 27.43 -65.44 REMARK 500 GLN B 96 -3.17 -150.22 REMARK 500 ARG B 97 46.31 35.52 REMARK 500 LEU B 128 -20.81 35.57 REMARK 500 ASN C 82 53.75 39.72 REMARK 500 GLN C 96 -2.42 -159.45 REMARK 500 ARG C 97 56.11 16.47 REMARK 500 LEU C 128 -92.26 45.13 REMARK 500 PRO D 86 150.87 -48.72 REMARK 500 GLU D 91 -71.85 -36.33 REMARK 500 ASN D 95 47.71 -76.52 REMARK 500 GLN D 96 -6.12 -142.92 REMARK 500 ARG D 97 39.86 37.18 REMARK 500 SER D 127 -107.18 -75.04 REMARK 500 LEU D 128 -34.09 113.90 REMARK 500 ASN E 82 55.84 37.72 REMARK 500 ASN E 95 48.22 -66.13 REMARK 500 GLN E 96 -17.63 -144.87 REMARK 500 ARG E 97 54.34 35.00 REMARK 500 SER E 127 -72.37 -93.10 REMARK 500 LEU E 128 121.44 45.19 REMARK 500 ASN F 95 43.26 -60.85 REMARK 500 GLN F 96 -13.26 -140.11 REMARK 500 ARG F 97 47.98 33.29 REMARK 500 LEU F 128 36.20 -173.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZAE RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PHI29 REPLICATION REMARK 900 ORGANIZER P16.7C REMARK 900 RELATED ID: 2BNK RELATED DB: PDB REMARK 900 THE STRUCTURE OF PHAGE PHI29 REPLICATION ORGANIZER PROTEIN P16.7 DBREF 2C5R A 63 129 UNP P16517 VG167_BPPH2 64 130 DBREF 2C5R B 63 129 UNP P16517 VG167_BPPH2 64 130 DBREF 2C5R C 63 129 UNP P16517 VG167_BPPH2 64 130 DBREF 2C5R D 63 129 UNP P16517 VG167_BPPH2 64 130 DBREF 2C5R E 63 129 UNP P16517 VG167_BPPH2 64 130 DBREF 2C5R F 63 129 UNP P16517 VG167_BPPH2 64 130 DBREF 2C5R Y 9 16 PDB 2C5R 2C5R 9 16 DBREF 2C5R Z 1 8 PDB 2C5R 2C5R 1 8 SEQRES 1 A 67 LYS THR VAL ASN LEU SER ALA CYS GLU VAL ALA VAL LEU SEQRES 2 A 67 ASP LEU TYR GLU GLN SER ASN ILE ARG ILE PRO SER ASP SEQRES 3 A 67 ILE ILE GLU ASP LEU VAL ASN GLN ARG LEU GLN SER GLU SEQRES 4 A 67 GLN GLU VAL LEU ASN TYR ILE GLU THR GLN ARG THR TYR SEQRES 5 A 67 TRP LYS LEU GLU ASN GLN LYS LYS LEU TYR ARG GLY SER SEQRES 6 A 67 LEU LYS SEQRES 1 B 67 LYS THR VAL ASN LEU SER ALA CYS GLU VAL ALA VAL LEU SEQRES 2 B 67 ASP LEU TYR GLU GLN SER ASN ILE ARG ILE PRO SER ASP SEQRES 3 B 67 ILE ILE GLU ASP LEU VAL ASN GLN ARG LEU GLN SER GLU SEQRES 4 B 67 GLN GLU VAL LEU ASN TYR ILE GLU THR GLN ARG THR TYR SEQRES 5 B 67 TRP LYS LEU GLU ASN GLN LYS LYS LEU TYR ARG GLY SER SEQRES 6 B 67 LEU LYS SEQRES 1 C 67 LYS THR VAL ASN LEU SER ALA CYS GLU VAL ALA VAL LEU SEQRES 2 C 67 ASP LEU TYR GLU GLN SER ASN ILE ARG ILE PRO SER ASP SEQRES 3 C 67 ILE ILE GLU ASP LEU VAL ASN GLN ARG LEU GLN SER GLU SEQRES 4 C 67 GLN GLU VAL LEU ASN TYR ILE GLU THR GLN ARG THR TYR SEQRES 5 C 67 TRP LYS LEU GLU ASN GLN LYS LYS LEU TYR ARG GLY SER SEQRES 6 C 67 LEU LYS SEQRES 1 D 67 LYS THR VAL ASN LEU SER ALA CYS GLU VAL ALA VAL LEU SEQRES 2 D 67 ASP LEU TYR GLU GLN SER ASN ILE ARG ILE PRO SER ASP SEQRES 3 D 67 ILE ILE GLU ASP LEU VAL ASN GLN ARG LEU GLN SER GLU SEQRES 4 D 67 GLN GLU VAL LEU ASN TYR ILE GLU THR GLN ARG THR TYR SEQRES 5 D 67 TRP LYS LEU GLU ASN GLN LYS LYS LEU TYR ARG GLY SER SEQRES 6 D 67 LEU LYS SEQRES 1 E 67 LYS THR VAL ASN LEU SER ALA CYS GLU VAL ALA VAL LEU SEQRES 2 E 67 ASP LEU TYR GLU GLN SER ASN ILE ARG ILE PRO SER ASP SEQRES 3 E 67 ILE ILE GLU ASP LEU VAL ASN GLN ARG LEU GLN SER GLU SEQRES 4 E 67 GLN GLU VAL LEU ASN TYR ILE GLU THR GLN ARG THR TYR SEQRES 5 E 67 TRP LYS LEU GLU ASN GLN LYS LYS LEU TYR ARG GLY SER SEQRES 6 E 67 LEU LYS SEQRES 1 F 67 LYS THR VAL ASN LEU SER ALA CYS GLU VAL ALA VAL LEU SEQRES 2 F 67 ASP LEU TYR GLU GLN SER ASN ILE ARG ILE PRO SER ASP SEQRES 3 F 67 ILE ILE GLU ASP LEU VAL ASN GLN ARG LEU GLN SER GLU SEQRES 4 F 67 GLN GLU VAL LEU ASN TYR ILE GLU THR GLN ARG THR TYR SEQRES 5 F 67 TRP LYS LEU GLU ASN GLN LYS LYS LEU TYR ARG GLY SER SEQRES 6 F 67 LEU LYS SEQRES 1 Y 8 DT DC DC DA DC DC DG DG SEQRES 1 Z 8 DC DC DG DG DT DG DG DA FORMUL 9 HOH *51(H2 O) HELIX 1 1 SER A 68 SER A 81 1 14 HELIX 2 2 PRO A 86 ASN A 95 1 10 HELIX 3 3 SER A 100 ASN A 119 1 20 HELIX 4 4 SER B 68 SER B 81 1 14 HELIX 5 5 PRO B 86 ASN B 95 1 10 HELIX 6 6 SER B 100 LYS B 121 1 22 HELIX 7 7 SER C 68 SER C 81 1 14 HELIX 8 8 PRO C 86 ASN C 95 1 10 HELIX 9 9 SER C 100 LYS C 121 1 22 HELIX 10 10 SER D 68 SER D 81 1 14 HELIX 11 11 PRO D 86 ASN D 95 1 10 HELIX 12 12 SER D 100 ASN D 119 1 20 HELIX 13 13 SER E 68 SER E 81 1 14 HELIX 14 14 PRO E 86 ASN E 95 1 10 HELIX 15 15 SER E 100 LYS E 121 1 22 HELIX 16 16 SER F 68 SER F 81 1 14 HELIX 17 17 PRO F 86 ASN F 95 1 10 HELIX 18 18 SER F 100 LYS F 121 1 22 CRYST1 65.505 72.111 127.360 90.00 90.00 90.00 P 21 21 21 24 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 0.015266 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013868 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007852 0.00000 MTRIX1 1 -0.998550 -0.022810 0.048820 39.73845 1 MTRIX2 1 -0.028070 -0.553300 -0.832510 27.39048 1 MTRIX3 1 0.046010 -0.832670 0.551860 13.62338 1 MTRIX1 2 -0.998260 -0.026380 -0.052820 34.55003 1 MTRIX2 2 0.023690 -0.998420 0.050920 32.33890 1 MTRIX3 2 -0.054080 0.049580 0.997300 -0.19360 1 MTRIX1 3 0.993490 0.081240 -0.079820 -6.12134 1 MTRIX2 3 0.033380 0.462400 0.886040 6.05816 1 MTRIX3 3 0.108890 -0.882940 0.456680 13.32267 1 MTRIX1 4 -0.985940 -0.132660 0.101630 45.94772 1 MTRIX2 4 -0.158310 0.546680 -0.822240 12.68644 1 MTRIX3 4 0.053520 -0.826770 -0.559990 16.75061 1 MTRIX1 5 0.995660 0.047720 0.079880 4.79002 1 MTRIX2 5 0.050320 0.445920 -0.893660 10.35376 1 MTRIX3 5 -0.078270 0.893800 0.441580 -11.41956 1