HEADER VIRAL PROTEIN 24-MAR-09 3GQ9 TITLE CRYSTAL STRUCTURE OF THE BACTERIOPHAGE PHI29 GENE PRODUCT 12 N- TITLE 2 TERMINAL FRAGMENT IN AN APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRENECK APPENDAGE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: D1*D2D3, RESIDUES 89-691; 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 HELIX, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.XIANG,M.G.ROSSMANN REVDAT 4 21-FEB-24 3GQ9 1 REMARK SEQADV LINK REVDAT 3 01-NOV-17 3GQ9 1 REMARK REVDAT 2 21-MAR-12 3GQ9 1 JRNL VERSN REVDAT 1 26-MAY-09 3GQ9 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 61145 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3077 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4149 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 212 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4478 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 363 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.28000 REMARK 3 B22 (A**2) : 0.28000 REMARK 3 B33 (A**2) : -0.41000 REMARK 3 B12 (A**2) : 0.14000 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): 0.127 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.122 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.076 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.745 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4655 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6338 ; 1.262 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 634 ; 6.775 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 205 ;39.273 ;24.439 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 739 ;12.088 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;15.719 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 721 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3586 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2190 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3275 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 361 ; 0.116 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.137 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 172 ; 0.172 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 42 ; 0.123 ; 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): 3011 ; 0.493 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4851 ; 0.967 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1681 ; 1.816 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1471 ; 2.975 ; 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 : NULL 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 : 1.20 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 3GQ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000052178. 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 : 10.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE-CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61778 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 43.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.3020 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.39700 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM CHES AT ~PH 10.0 AND 8% PEG3K. REMARK 280 CRYSTALLS OBTAINED WERE THEN SOAKED IN A MOTHER LIQUID REMARK 280 CONTAINING 10MM EDTA FOR ~5 HOURS., VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 44.81650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 25.87482 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 195.23967 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 44.81650 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 25.87482 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 195.23967 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 44.81650 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 25.87482 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 195.23967 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 44.81650 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 25.87482 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 195.23967 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 44.81650 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 25.87482 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 195.23967 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 44.81650 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 25.87482 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 195.23967 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 51.74964 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 390.47933 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 51.74964 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 390.47933 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 51.74964 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 390.47933 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 51.74964 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 390.47933 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 51.74964 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 390.47933 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 51.74964 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 390.47933 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 27760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 47380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -202.0 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 -0.500000 -0.866025 0.000000 89.63300 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 44.81650 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 77.62446 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 56780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 93510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -420.0 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 -0.500000 -0.866025 0.000000 89.63300 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 44.81650 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 77.62446 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000000 44.81650 REMARK 350 BIOMT2 4 0.866025 0.500000 0.000000 -25.87482 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 390.47933 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 -1.000000 0.000000 51.74964 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 390.47933 REMARK 350 BIOMT1 6 -0.500000 -0.866025 0.000000 89.63300 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 51.74964 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 390.47933 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 HIS A 83 REMARK 465 HIS A 84 REMARK 465 HIS A 85 REMARK 465 HIS A 86 REMARK 465 HIS A 87 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 VAL A 117 -53.66 -133.92 REMARK 500 ASN A 162 -70.83 -128.42 REMARK 500 ASN A 189 71.62 62.61 REMARK 500 SER A 194 61.48 63.81 REMARK 500 GLU A 216 27.99 83.13 REMARK 500 ASN A 226 69.75 70.76 REMARK 500 LEU A 239 -102.37 -100.12 REMARK 500 ASN A 266 73.83 62.98 REMARK 500 ASP A 279 -91.36 -120.12 REMARK 500 TYR A 289 70.24 65.70 REMARK 500 ASP A 299 74.12 55.99 REMARK 500 ALA A 304 -145.16 -86.36 REMARK 500 ASP A 313 115.03 -16.63 REMARK 500 TYR A 329 -75.98 -74.06 REMARK 500 ASP A 339 36.27 -98.81 REMARK 500 ASN A 380 89.49 65.39 REMARK 500 ALA A 410 -35.57 68.18 REMARK 500 GLU A 431 -82.62 -97.69 REMARK 500 SER A 591 45.88 39.94 REMARK 500 ARG A 598 82.32 68.62 REMARK 500 GLU A 665 -15.23 69.87 REMARK 500 ASP A 682 -107.69 -94.80 REMARK 500 TRP A 690 63.47 -116.03 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 NA A 1 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 279 OD2 REMARK 620 2 ASP A 280 OD1 96.0 REMARK 620 3 ASP A 280 OD2 85.0 52.7 REMARK 620 4 ASN A 305 O 82.2 91.4 140.2 REMARK 620 5 GLU A 310 OE1 155.6 83.6 75.3 122.2 REMARK 620 6 HOH A 935 O 75.5 140.8 88.2 124.1 89.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 692 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 64 O REMARK 620 2 HOH A 80 O 87.9 REMARK 620 3 ASP A 312 OD2 92.8 107.6 REMARK 620 4 HOH A 935 O 106.6 118.3 130.1 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 NA A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 692 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NHE A 693 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: 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: 3GQK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BACTERIOPHAGE PHI29 GENE PRODUCT 12 C- REMARK 900 TERMINAL FRAGMENT IN COMPLEX WITH ATP 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 3GQ9 A 89 691 UNP B3VMP8 B3VMP8_BPPH2 89 691 SEQADV 3GQ9 HIS A 83 UNP B3VMP8 EXPRESSION TAG SEQADV 3GQ9 HIS A 84 UNP B3VMP8 EXPRESSION TAG SEQADV 3GQ9 HIS A 85 UNP B3VMP8 EXPRESSION TAG SEQADV 3GQ9 HIS A 86 UNP B3VMP8 EXPRESSION TAG SEQADV 3GQ9 HIS A 87 UNP B3VMP8 EXPRESSION TAG SEQADV 3GQ9 HIS A 88 UNP B3VMP8 EXPRESSION TAG SEQADV 3GQ9 ARG A 166 UNP B3VMP8 LYS 166 SEE REMARK 999 SEQADV 3GQ9 GLN A 627 UNP B3VMP8 LYS 627 SEE REMARK 999 SEQRES 1 A 609 HIS HIS HIS HIS HIS HIS PHE ALA ASP LEU VAL ILE GLN SEQRES 2 A 609 VAL ILE ASP GLU LEU LYS GLN PHE GLY VAL SER VAL LYS SEQRES 3 A 609 THR TYR GLY ALA LYS GLY ASP GLY VAL THR ASP ASP ILE SEQRES 4 A 609 ARG ALA PHE GLU LYS ALA ILE GLU SER GLY PHE PRO VAL SEQRES 5 A 609 TYR VAL PRO TYR GLY THR PHE MET VAL SER ARG GLY ILE SEQRES 6 A 609 LYS LEU PRO SER ASN THR VAL LEU THR GLY ALA GLY LYS SEQRES 7 A 609 ARG ASN ALA VAL ILE ARG PHE MET ASP SER VAL GLY ARG SEQRES 8 A 609 GLY GLU SER LEU MET TYR ASN GLU ASN VAL THR THR GLY SEQRES 9 A 609 ASN GLU ASN ILE PHE LEU SER SER PHE THR LEU ASP GLY SEQRES 10 A 609 ASN ASN LYS ARG LEU GLY GLN GLY ILE SER GLY ILE GLY SEQRES 11 A 609 GLY SER ARG GLU SER ASN LEU SER ILE ARG ALA CYS HIS SEQRES 12 A 609 ASN VAL TYR ILE ARG ASP ILE GLU ALA VAL ASP CYS THR SEQRES 13 A 609 LEU HIS GLY ILE ASP ILE THR CYS GLY GLY LEU ASP TYR SEQRES 14 A 609 PRO TYR LEU GLY ASP GLY THR THR ALA PRO ASN PRO SER SEQRES 15 A 609 GLU ASN ILE TRP ILE GLU ASN CYS GLU ALA THR GLY PHE SEQRES 16 A 609 GLY ASP ASP GLY ILE THR THR HIS HIS SER GLN TYR ILE SEQRES 17 A 609 ASN ILE LEU ASN CYS TYR SER HIS ASP PRO ARG LEU THR SEQRES 18 A 609 ALA ASN CYS ASN GLY PHE GLU ILE ASP ASP GLY SER ARG SEQRES 19 A 609 HIS VAL VAL LEU SER ASN ASN ARG SER LYS GLY CYS TYR SEQRES 20 A 609 GLY GLY ILE GLU ILE LYS ALA HIS GLY ASP ALA PRO ALA SEQRES 21 A 609 ALA TYR ASN ILE SER ILE ASN GLY HIS MET SER VAL GLU SEQRES 22 A 609 ASP VAL ARG SER TYR ASN PHE ARG HIS ILE GLY HIS HIS SEQRES 23 A 609 ALA ALA THR ALA PRO GLN SER VAL SER ALA LYS ASN ILE SEQRES 24 A 609 VAL ALA SER ASN LEU VAL SER ILE ARG PRO ASN ASN LYS SEQRES 25 A 609 ARG GLY PHE GLN ASP ASN ALA THR PRO ARG VAL LEU ALA SEQRES 26 A 609 VAL SER ALA TYR TYR GLY VAL VAL ILE ASN GLY LEU THR SEQRES 27 A 609 GLY TYR THR ASP ASP PRO ASN LEU LEU THR GLU THR VAL SEQRES 28 A 609 VAL SER VAL GLN PHE ARG ALA ARG ASN CYS SER LEU ASN SEQRES 29 A 609 GLY VAL VAL LEU THR GLY PHE SER ASN SER GLU ASN GLY SEQRES 30 A 609 ILE TYR VAL ILE GLY GLY SER ARG GLY GLY ASP ALA VAL SEQRES 31 A 609 ASN ILE SER ASN VAL THR LEU ASN ASN SER GLY ARG TYR SEQRES 32 A 609 GLY VAL SER ILE GLY SER GLY ILE GLU ASN VAL SER ILE SEQRES 33 A 609 THR ASN ILE SER GLY ILE GLY ASP GLY ILE ASN SER PRO SEQRES 34 A 609 VAL ALA LEU VAL SER THR ILE ASN SER ASN PRO GLU ILE SEQRES 35 A 609 SER GLY LEU SER SER ILE GLY TYR PRO THR VAL ALA ARG SEQRES 36 A 609 VAL ALA GLY THR ASP TYR ASN ASP GLY LEU THR LEU PHE SEQRES 37 A 609 ASN GLY ALA PHE ARG ALA SER THR THR SER SER GLY LYS SEQRES 38 A 609 ILE HIS SER GLU GLY PHE ILE MET GLY SER THR SER GLY SEQRES 39 A 609 CYS GLU ALA SER VAL SER LYS SER GLY VAL LEU THR SER SEQRES 40 A 609 SER SER SER LYS THR SER SER GLU ARG SER LEU ILE ALA SEQRES 41 A 609 GLY SER SER THR SER GLU ALA LYS GLY THR TYR ASN THR SEQRES 42 A 609 ILE LEU GLY SER LEU GLY ALA VAL ALA ASP GLU GLN PHE SEQRES 43 A 609 ALA ALA LEU ILE SER ALA SER GLN SER ARG ALA SER GLY SEQRES 44 A 609 ASN HIS ASN LEU ILE LEU SER SER TYR GLY ILE ASN THR SEQRES 45 A 609 THR GLY SER TYR LYS VAL ASN GLY GLY PHE GLU LYS ILE SEQRES 46 A 609 ASN TRP GLU LEU ASP SER LEU ASN GLY ARG ILE LYS ALA SEQRES 47 A 609 ARG ASP THR VAL THR GLY GLY ASN THR TRP SER HET NA A 1 1 HET NA A 692 1 HET NHE A 693 13 HETNAM NA SODIUM ION HETNAM NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID HETSYN NHE N-CYCLOHEXYLTAURINE; CHES FORMUL 2 NA 2(NA 1+) FORMUL 4 NHE C8 H17 N O3 S FORMUL 5 HOH *363(H2 O) HELIX 1 1 HIS A 88 LYS A 101 1 14 HELIX 2 2 LYS A 108 GLY A 111 5 4 HELIX 3 3 ASP A 120 SER A 130 1 11 HELIX 4 4 ASN A 200 GLY A 205 5 6 HELIX 5 5 GLY A 396 ALA A 401 1 6 SHEET 1 A 9 VAL A 105 SER A 106 0 SHEET 2 A 9 VAL A 134 VAL A 136 1 O TYR A 135 N VAL A 105 SHEET 3 A 9 THR A 153 GLY A 157 1 O VAL A 154 N VAL A 134 SHEET 4 A 9 GLU A 188 ASP A 198 1 O PHE A 191 N LEU A 155 SHEET 5 A 9 HIS A 225 VAL A 235 1 O GLU A 233 N LEU A 197 SHEET 6 A 9 GLU A 265 GLU A 270 1 O TRP A 268 N ILE A 229 SHEET 7 A 9 GLN A 288 LEU A 293 1 O ASN A 291 N ILE A 269 SHEET 8 A 9 ARG A 316 LYS A 326 1 O VAL A 319 N ILE A 292 SHEET 9 A 9 TYR A 296 HIS A 298 1 N SER A 297 O ARG A 324 SHEET 1 B15 ASP A 115 ASP A 119 0 SHEET 2 B15 GLY A 139 VAL A 143 1 O THR A 140 N GLY A 116 SHEET 3 B15 ALA A 163 PHE A 167 1 O VAL A 164 N PHE A 141 SHEET 4 B15 GLU A 188 ASP A 198 1 O ASP A 198 N ILE A 165 SHEET 5 B15 HIS A 225 VAL A 235 1 O GLU A 233 N LEU A 197 SHEET 6 B15 GLU A 273 THR A 275 1 O GLU A 273 N ALA A 234 SHEET 7 B15 TYR A 296 HIS A 298 1 O HIS A 298 N ALA A 274 SHEET 8 B15 ARG A 316 LYS A 326 1 O ARG A 324 N SER A 297 SHEET 9 B15 TYR A 344 VAL A 354 1 O ASN A 349 N LEU A 320 SHEET 10 B15 LYS A 379 ILE A 389 1 O SER A 384 N ILE A 348 SHEET 11 B15 TYR A 412 TYR A 422 1 O VAL A 415 N ALA A 383 SHEET 12 B15 ARG A 441 THR A 451 1 O SER A 444 N ILE A 416 SHEET 13 B15 VAL A 472 ASN A 480 1 O ASN A 480 N LEU A 450 SHEET 14 B15 VAL A 496 ILE A 504 1 O SER A 497 N ILE A 474 SHEET 15 B15 GLU A 523 ILE A 530 1 O GLU A 523 N ILE A 498 SHEET 1 C15 ILE A 147 LEU A 149 0 SHEET 2 C15 MET A 178 ASN A 180 1 O TYR A 179 N LEU A 149 SHEET 3 C15 LEU A 219 ARG A 222 1 O SER A 220 N MET A 178 SHEET 4 C15 ILE A 242 THR A 245 1 O THR A 245 N ILE A 221 SHEET 5 C15 ILE A 282 THR A 284 1 O THR A 283 N ILE A 242 SHEET 6 C15 PHE A 309 ILE A 311 1 O GLU A 310 N ILE A 282 SHEET 7 C15 GLY A 330 ILE A 334 1 O GLU A 333 N ILE A 311 SHEET 8 C15 ARG A 358 PHE A 362 1 O SER A 359 N ILE A 332 SHEET 9 C15 ARG A 404 SER A 409 1 O ALA A 407 N PHE A 362 SHEET 10 C15 THR A 432 GLN A 437 1 O VAL A 433 N VAL A 405 SHEET 11 C15 ASN A 458 VAL A 462 1 O TYR A 461 N VAL A 434 SHEET 12 C15 TYR A 485 ILE A 489 1 O SER A 488 N ILE A 460 SHEET 13 C15 ALA A 513 THR A 517 1 O SER A 516 N ILE A 489 SHEET 14 C15 THR A 534 VAL A 538 1 O ARG A 537 N VAL A 515 SHEET 15 C15 THR A 541 TYR A 543 -1 O THR A 541 N VAL A 538 SHEET 1 D 7 PHE A 554 ALA A 556 0 SHEET 2 D 7 GLY A 568 MET A 571 1 O ILE A 570 N ALA A 556 SHEET 3 D 7 SER A 584 LEU A 587 1 O VAL A 586 N MET A 571 SHEET 4 D 7 GLU A 597 ALA A 602 1 O ILE A 601 N LEU A 587 SHEET 5 D 7 THR A 612 LEU A 617 1 O ILE A 616 N ALA A 602 SHEET 6 D 7 ALA A 630 ALA A 639 1 O LEU A 631 N LEU A 617 SHEET 7 D 7 ASN A 653 THR A 654 1 O THR A 654 N ARG A 638 SHEET 1 E 9 GLU A 578 ALA A 579 0 SHEET 2 E 9 LYS A 593 THR A 594 1 O THR A 594 N GLU A 578 SHEET 3 E 9 GLU A 608 ALA A 609 1 O ALA A 609 N LYS A 593 SHEET 4 E 9 LEU A 620 ALA A 624 1 O ALA A 622 N GLU A 608 SHEET 5 E 9 ALA A 630 ALA A 639 1 O GLN A 636 N LEU A 620 SHEET 6 E 9 LEU A 645 TYR A 650 1 O ILE A 646 N ILE A 632 SHEET 7 E 9 LYS A 659 GLY A 663 1 O ASN A 661 N LEU A 645 SHEET 8 E 9 ILE A 667 ASP A 672 -1 O LEU A 671 N VAL A 660 SHEET 9 E 9 ARG A 677 ALA A 680 -1 O ARG A 677 N ASP A 672 LINK NA NA A 1 OD2 ASP A 279 1555 1555 2.55 LINK NA NA A 1 OD1 ASP A 280 1555 1555 2.45 LINK NA NA A 1 OD2 ASP A 280 1555 1555 2.50 LINK NA NA A 1 O ASN A 305 1555 1555 2.30 LINK NA NA A 1 OE1 GLU A 310 1555 1555 2.55 LINK NA NA A 1 O HOH A 935 1555 1555 2.37 LINK O HOH A 64 NA NA A 692 1555 1555 2.35 LINK O HOH A 80 NA NA A 692 1555 1555 2.18 LINK OD2 ASP A 312 NA NA A 692 1555 1555 2.25 LINK NA NA A 692 O HOH A 935 1555 1555 2.46 SITE 1 AC1 6 ASP A 279 ASP A 280 ASN A 305 ASN A 307 SITE 2 AC1 6 GLU A 310 HOH A 935 SITE 1 AC2 7 HOH A 64 HOH A 80 ASP A 280 HIS A 285 SITE 2 AC2 7 GLU A 310 ASP A 312 HOH A 935 SITE 1 AC3 9 ARG A 358 HIS A 368 THR A 402 ARG A 404 SITE 2 AC3 9 GLU A 431 GLN A 437 TYR A 650 HOH A 856 SITE 3 AC3 9 HOH A 951 CRYST1 89.633 89.633 585.719 90.00 90.00 120.00 H 3 2 18 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 0.011157 0.006441 0.000000 0.00000 SCALE2 0.000000 0.012883 0.000000 0.00000 SCALE3 0.000000 0.000000 0.001707 0.00000