HEADER VIRAL PROTEIN 27-JUL-09 3IGE TITLE SMALL OUTER CAPSID PROTEIN (SOC) FROM BACTERIOPHAGE RB69 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOC SMALL OUTER CAPSID PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE RB69; SOURCE 3 ORGANISM_COMMON: BACTERIOPHAGE RB69; SOURCE 4 ORGANISM_TAXID: 12353; SOURCE 5 GENE: SOC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: T7 EXPRESSION VECTOR, PET28B KEYWDS ALPHA/BETA PROTEIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Q.LI,A.FOKINE,E.O'DONNELL,V.B.RAO,M.G.ROSSMANN REVDAT 4 03-APR-24 3IGE 1 REMARK REVDAT 3 21-FEB-24 3IGE 1 REMARK REVDAT 2 09-FEB-10 3IGE 1 JRNL REVDAT 1 08-DEC-09 3IGE 0 JRNL AUTH L.QIN,A.FOKINE,E.O'DONNELL,V.B.RAO,M.G.ROSSMANN JRNL TITL STRUCTURE OF THE SMALL OUTER CAPSID PROTEIN, SOC: A CLAMP JRNL TITL 2 FOR STABILIZING CAPSIDS OF T4-LIKE PHAGES JRNL REF J.MOL.BIOL. V. 395 728 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 19835886 JRNL DOI 10.1016/J.JMB.2009.10.007 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 7023 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 334 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 23.5959 - 2.8396 1.00 3403 167 0.1976 0.2235 REMARK 3 2 2.8396 - 2.2545 1.00 3286 167 0.2559 0.3513 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 40.41 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 1212 REMARK 3 ANGLE : 0.421 1648 REMARK 3 CHIRALITY : 0.030 178 REMARK 3 PLANARITY : 0.003 214 REMARK 3 DIHEDRAL : 11.300 414 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -8.3400 40.8117 11.6614 REMARK 3 T TENSOR REMARK 3 T11: 0.2889 T22: 0.1479 REMARK 3 T33: 0.1238 T12: -0.0268 REMARK 3 T13: -0.0446 T23: -0.0119 REMARK 3 L TENSOR REMARK 3 L11: 2.2342 L22: 2.3718 REMARK 3 L33: 1.0355 L12: 0.2625 REMARK 3 L13: 0.8136 L23: 1.1673 REMARK 3 S TENSOR REMARK 3 S11: 0.2301 S12: 0.0658 S13: -0.1947 REMARK 3 S21: -0.1277 S22: -0.1324 S23: -0.0603 REMARK 3 S31: 0.4588 S32: -0.1272 S33: -0.0870 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3IGE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054377. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7033 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.540 REMARK 200 RESOLUTION RANGE LOW (A) : 23.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05800 REMARK 200 FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: STRUCTURE OF THE SOC PROTEIN FROM BACTERIOPHAGE REMARK 200 RB69 (HEXAGONAL CRYSTAL FORM). REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 8000; 0.1 M IMIDAZOLE; 0.2 M REMARK 280 NACL., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K, PH 8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.97200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.97200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 19.61000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.30650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 19.61000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.30650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.97200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 19.61000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.30650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 40.97200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 19.61000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.30650 REMARK 290 SMTRY3 8 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 300 REMARK: AUTHORS STATE THAT THE PROTEIN FORMS TRIMERS IN VIRUS BUT REMARK 300 IS MONOMER IN SOLUTION. 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 1 REMARK 465 SER A 77 REMARK 465 GLY A 78 REMARK 465 MET B 1 REMARK 465 SER B 77 REMARK 465 GLY B 78 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 ALA B 14 61.27 -117.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IG9 RELATED DB: PDB DBREF 3IGE A 1 78 UNP Q7Y5B1 Q7Y5B1_BPR69 1 78 DBREF 3IGE B 1 78 UNP Q7Y5B1 Q7Y5B1_BPR69 1 78 SEQRES 1 A 78 MET GLY GLY TYR VAL ASN ILE LYS THR PHE THR HIS PRO SEQRES 2 A 78 ALA GLY GLU GLY LYS GLU VAL LYS GLY MET GLU VAL SER SEQRES 3 A 78 VAL PRO PHE GLU ILE TYR SER ASN GLU HIS ARG ILE ALA SEQRES 4 A 78 ASP ALA HIS TYR GLN THR PHE PRO SER GLU LYS ALA ALA SEQRES 5 A 78 TYR THR THR VAL VAL THR ASP ALA ALA ASP TRP ARG THR SEQRES 6 A 78 LYS ASN ALA ALA MET PHE THR PRO THR PRO VAL SER GLY SEQRES 1 B 78 MET GLY GLY TYR VAL ASN ILE LYS THR PHE THR HIS PRO SEQRES 2 B 78 ALA GLY GLU GLY LYS GLU VAL LYS GLY MET GLU VAL SER SEQRES 3 B 78 VAL PRO PHE GLU ILE TYR SER ASN GLU HIS ARG ILE ALA SEQRES 4 B 78 ASP ALA HIS TYR GLN THR PHE PRO SER GLU LYS ALA ALA SEQRES 5 B 78 TYR THR THR VAL VAL THR ASP ALA ALA ASP TRP ARG THR SEQRES 6 B 78 LYS ASN ALA ALA MET PHE THR PRO THR PRO VAL SER GLY HET IMD A 100 5 HET IMD B 101 5 HETNAM IMD IMIDAZOLE FORMUL 3 IMD 2(C3 H5 N2 1+) FORMUL 5 HOH *120(H2 O) HELIX 1 1 PHE A 29 GLU A 35 1 7 HELIX 2 2 ASP A 59 ALA A 69 1 11 HELIX 3 3 PHE B 29 GLU B 35 1 7 HELIX 4 4 ASP B 59 MET B 70 1 12 SHEET 1 A 4 TYR A 43 SER A 48 0 SHEET 2 A 4 TYR A 4 THR A 9 -1 N TYR A 4 O SER A 48 SHEET 3 A 4 MET A 23 PRO A 28 -1 O VAL A 27 N VAL A 5 SHEET 4 A 4 THR A 55 VAL A 56 1 O THR A 55 N SER A 26 SHEET 1 B 3 HIS A 12 PRO A 13 0 SHEET 2 B 3 LYS A 18 VAL A 20 -1 O VAL A 20 N HIS A 12 SHEET 3 B 3 THR A 74 PRO A 75 -1 O THR A 74 N GLU A 19 SHEET 1 C 4 TYR B 43 SER B 48 0 SHEET 2 C 4 TYR B 4 THR B 9 -1 N TYR B 4 O SER B 48 SHEET 3 C 4 GLU B 24 PRO B 28 -1 O VAL B 25 N ILE B 7 SHEET 4 C 4 THR B 55 VAL B 56 1 O THR B 55 N SER B 26 SHEET 1 D 3 HIS B 12 PRO B 13 0 SHEET 2 D 3 LYS B 18 VAL B 20 -1 O VAL B 20 N HIS B 12 SHEET 3 D 3 THR B 74 PRO B 75 -1 O THR B 74 N GLU B 19 SITE 1 AC1 5 TYR A 32 ARG A 37 TYR A 43 MET A 70 SITE 2 AC1 5 HOH A 109 SITE 1 AC2 5 TYR B 32 ARG B 37 ILE B 38 TYR B 43 SITE 2 AC2 5 HOH B 128 CRYST1 39.220 88.613 81.944 90.00 90.00 90.00 C 2 2 21 16 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 0.025497 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011285 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012203 0.00000