HEADER VIRAL PROTEIN 24-MAR-09 3GQK TITLE CRYSTAL STRUCTURE OF THE BACTERIOPHAGE PHI29 GENE PRODUCT 12 C- TITLE 2 TERMINAL FRAGMENT IN COMPLEX WITH ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRENECK APPENDAGE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: D4, RESIDUES 692-854; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS PHAGE PHI29; SOURCE 3 ORGANISM_TAXID: 10756; SOURCE 4 GENE: 12, GENE PRODUCT 12; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS BETA BARREL, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.XIANG,M.G.ROSSMANN REVDAT 5 06-SEP-23 3GQK 1 REMARK REVDAT 4 01-NOV-17 3GQK 1 REMARK REVDAT 3 21-MAR-12 3GQK 1 JRNL REVDAT 2 13-JUL-11 3GQK 1 VERSN REVDAT 1 26-MAY-09 3GQK 0 JRNL AUTH Y.XIANG,P.G.LEIMAN,L.LI,S.GRIMES,D.L.ANDERSON,M.G.ROSSMANN JRNL TITL CRYSTALLOGRAPHIC INSIGHTS INTO THE AUTOCATALYTIC ASSEMBLY JRNL TITL 2 MECHANISM OF A BACTERIOPHAGE TAIL SPIKE. JRNL REF MOL.CELL V. 34 375 2009 JRNL REFN ISSN 1097-2765 JRNL PMID 19450535 JRNL DOI 10.1016/J.MOLCEL.2009.04.009 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 7244 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) : 0.267 REMARK 3 R VALUE (WORKING SET) : 0.264 REMARK 3 FREE R VALUE : 0.334 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 334 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 497 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4090 REMARK 3 BIN FREE R VALUE SET COUNT : 27 REMARK 3 BIN FREE R VALUE : 0.5170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1274 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 3 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) : 43.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.596 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.371 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.343 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 30.871 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.880 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1332 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1808 ; 1.430 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 162 ; 8.459 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 60 ;41.054 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 226 ;18.461 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ; 9.560 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 197 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 997 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 562 ; 0.231 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 905 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 52 ; 0.177 ; 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): 45 ; 0.267 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.117 ; 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): 826 ; 0.687 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1294 ; 1.171 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 584 ; 1.827 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 514 ; 2.998 ; 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 : NULL 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 692 A 741 REMARK 3 RESIDUE RANGE : A 789 A 854 REMARK 3 ORIGIN FOR THE GROUP (A): -0.7465 19.0700 1.8037 REMARK 3 T TENSOR REMARK 3 T11: 0.4876 T22: 0.0179 REMARK 3 T33: 0.4610 T12: 0.0167 REMARK 3 T13: 0.1070 T23: 0.0126 REMARK 3 L TENSOR REMARK 3 L11: 7.4042 L22: 9.0510 REMARK 3 L33: 7.9865 L12: -0.4503 REMARK 3 L13: -1.5361 L23: -1.4640 REMARK 3 S TENSOR REMARK 3 S11: 0.4177 S12: -0.0036 S13: 1.7341 REMARK 3 S21: 0.7739 S22: 0.0597 S23: -0.0182 REMARK 3 S31: -1.7669 S32: -0.0100 S33: -0.4774 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 742 A 788 REMARK 3 ORIGIN FOR THE GROUP (A): -20.0481 -7.5244 11.7136 REMARK 3 T TENSOR REMARK 3 T11: 0.6187 T22: 0.7680 REMARK 3 T33: 0.7068 T12: 0.0302 REMARK 3 T13: 0.0674 T23: 0.1851 REMARK 3 L TENSOR REMARK 3 L11: 4.6388 L22: 6.1614 REMARK 3 L33: 5.0581 L12: 3.5675 REMARK 3 L13: -1.3456 L23: -5.0290 REMARK 3 S TENSOR REMARK 3 S11: 0.2854 S12: 0.5522 S13: 0.5995 REMARK 3 S21: -0.6643 S22: 0.3602 S23: 1.4251 REMARK 3 S31: 0.6792 S32: -0.9961 S33: -0.6456 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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: NULL REMARK 4 REMARK 4 3GQK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000052189. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE-CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7288 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 26.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 56.4730 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.10 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3GQH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM BIS-TRIS AT PH 7.0, 20% PEG4K, REMARK 280 10%V/V MPD, 10MM MGCL2 AND 10MM ATP, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 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 42.60550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.60550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.60550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.60550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.60550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.60550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 42.60550 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 42.60550 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 42.60550 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 42.60550 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 42.60550 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 42.60550 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 42.60550 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 42.60550 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 42.60550 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 42.60550 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 42.60550 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 42.60550 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 BIOMT1 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 0.00000 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 SER A 743 N - CA - C ANGL. DEV. = 16.7 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 GLN A 703 -155.57 -52.64 REMARK 500 LYS A 715 60.08 37.07 REMARK 500 PHE A 744 -71.53 148.07 REMARK 500 GLN A 747 -19.06 -48.22 REMARK 500 ASN A 753 -167.09 -71.07 REMARK 500 THR A 765 -118.83 -137.54 REMARK 500 ASP A 767 13.38 49.76 REMARK 500 PHE A 831 -171.12 56.44 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 SER A 743 PHE A 744 -59.90 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 A 855 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A 1 O2G REMARK 620 2 ATP A 1 O1B 77.7 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 855 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GQ7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BACTERIOPHAGE PHI29 GENE PRODUCT 12 N- REMARK 900 TERMINAL FRAGMENT REMARK 900 RELATED ID: 3GQ8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BACTERIOPHAGE PHI29 GENE PRODUCT 12 N- REMARK 900 TERMINAL FRAGMENT IN COMPLEX WITH 2-(N-CYCLOHEXYLAMINO)ETHANE REMARK 900 SULFONIC ACID (CHES) REMARK 900 RELATED ID: 3GQ9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BACTERIOPHAGE PHI29 GENE PRODUCT 12 N- REMARK 900 TERMINAL FRAGMENT IN AN APO FORM REMARK 900 RELATED ID: 3GQA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BACTERIOPHAGE PHI29 GENE PRODUCT 12 N- REMARK 900 TERMINAL FRAGMENT IN COMPLEX WITH COBALT IONS REMARK 900 RELATED ID: 3GQH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BACTERIOPHAGE PHI29 GENE PRODUCT 12 C- REMARK 900 TERMINAL FRAGMENT REMARK 900 RELATED ID: 3GQN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PRE-MATURE BACTERIOPHAGE PHI29 GENE REMARK 900 PRODUCT 12 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THESE MUTATIONS MIGHT BE AN ACCUMULATED RESULT OF THE PHAGE REMARK 999 PASSAGING DBREF 3GQK A 692 854 UNP B3VMP8 B3VMP8_BPPH2 692 854 SEQADV 3GQK GLY A 701 UNP B3VMP8 ASP 701 SEE REMARK 999 SEQADV 3GQK SER A 817 UNP B3VMP8 GLY 817 SEE REMARK 999 SEQRES 1 A 163 ASP PHE ALA GLU TYR PHE GLU SER LEU GLY GLY GLN VAL SEQRES 2 A 163 ILE GLU THR GLY TYR LEU VAL THR LEU GLU LYS GLY LYS SEQRES 3 A 163 ILE ARG LYS ALA GLU LYS GLY GLU LYS ILE ILE GLY VAL SEQRES 4 A 163 ILE SER GLU THR ALA GLY PHE VAL LEU GLY GLU SER SER SEQRES 5 A 163 PHE GLU TRP GLN GLY ALA VAL LEU LYS ASN GLU PHE GLY SEQRES 6 A 163 GLY ILE ILE TYR GLU GLU VAL THR THR GLU ASP GLY VAL SEQRES 7 A 163 LYS PHE LYS ARG PRO LEU PRO ASN PRO ASP PHE ASP PRO SEQRES 8 A 163 ASN LYS ASN TYR ILE PRO ARG SER GLN ARG ARG GLU TRP SEQRES 9 A 163 HIS VAL VAL GLY LEU LEU GLY GLN ILE ALA VAL ARG ILE SEQRES 10 A 163 ASP GLU THR VAL LYS GLN GLY HIS SER ILE ASP ALA VAL SEQRES 11 A 163 GLY GLY VAL ALA THR ASP GLY ASP ASN PHE ILE VAL GLN SEQRES 12 A 163 GLU ILE THR THR PRO TYR THR LYS GLU LYS GLY TYR GLY SEQRES 13 A 163 VAL ALA ILE VAL LEU VAL LYS HET ATP A 1 31 HET MG A 855 1 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 MG MG 2+ FORMUL 4 HOH *3(H2 O) SHEET 1 A 6 LYS A 717 LYS A 720 0 SHEET 2 A 6 LEU A 710 GLU A 714 -1 N GLU A 714 O LYS A 717 SHEET 3 A 6 GLY A 729 ILE A 731 -1 O GLY A 729 N VAL A 711 SHEET 4 A 6 TRP A 795 ILE A 808 -1 O GLY A 799 N VAL A 730 SHEET 5 A 6 PHE A 693 GLU A 698 -1 N PHE A 697 O HIS A 796 SHEET 6 A 6 PHE A 737 LEU A 739 1 O LEU A 739 N TYR A 696 SHEET 1 B 6 LYS A 717 LYS A 720 0 SHEET 2 B 6 LEU A 710 GLU A 714 -1 N GLU A 714 O LYS A 717 SHEET 3 B 6 GLY A 729 ILE A 731 -1 O GLY A 729 N VAL A 711 SHEET 4 B 6 TRP A 795 ILE A 808 -1 O GLY A 799 N VAL A 730 SHEET 5 B 6 TYR A 846 VAL A 853 -1 O GLY A 847 N ILE A 808 SHEET 6 B 6 ILE A 832 THR A 841 -1 N THR A 837 O VAL A 848 SHEET 1 C 2 TYR A 760 VAL A 763 0 SHEET 2 C 2 PHE A 771 PRO A 774 -1 O PHE A 771 N VAL A 763 SHEET 1 D 2 ILE A 818 VAL A 821 0 SHEET 2 D 2 VAL A 824 ASN A 830 -1 O THR A 826 N ASP A 819 LINK O2G ATP A 1 MG MG A 855 1555 1555 2.33 LINK O1B ATP A 1 MG MG A 855 1555 1555 2.28 SITE 1 AC1 11 TRP A 746 GLN A 747 ASP A 779 ASP A 781 SITE 2 AC1 11 ASN A 785 TYR A 786 ILE A 787 ARG A 789 SITE 3 AC1 11 ARG A 792 TRP A 795 MG A 855 SITE 1 AC2 2 ATP A 1 GLU A 698 CRYST1 85.211 85.211 85.211 90.00 90.00 90.00 P 21 3 12 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 0.011736 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011736 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011736 0.00000