HEADER VIRAL PROTEIN 02-MAY-03 1P7N TITLE DIMERIC ROUS SARCOMA VIRUS CAPSID PROTEIN STRUCTURE WITH AN UPSTREAM TITLE 2 25-AMINO ACID RESIDUE EXTENSION OF C-TERMINAL OF GAG P10 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG POLYPROTEIN CAPSID PROTEIN P27; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ROUS SARCOMA VIRUS; SOURCE 3 ORGANISM_TAXID: 11886; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RETROVIRUS, CAPSID PROTEIN, GAG POLYPROTEIN, IMMATURE GAG, VIRAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.NANDHAGOPAL,A.A.SIMPSON,M.C.JOHNSON,A.B.FRANCISCO,G.W.SCHATZ, AUTHOR 2 M.G.ROSSMANN,V.M.VOGT REVDAT 4 16-AUG-23 1P7N 1 SEQADV REVDAT 3 13-JUL-11 1P7N 1 VERSN REVDAT 2 24-FEB-09 1P7N 1 VERSN REVDAT 1 23-DEC-03 1P7N 0 JRNL AUTH N.NANDHAGOPAL,A.A.SIMPSON,M.C.JOHNSON,A.B.FRANCISCO, JRNL AUTH 2 G.W.SCHATZ,M.G.ROSSMANN,V.M.VOGT JRNL TITL DIMERIC ROUS SARCOMA VIRUS CAPSID PROTEIN STRUCTURE RELEVANT JRNL TITL 2 TO IMMATURE GAG ASSEMBLY JRNL REF J.MOL.BIOL. V. 335 275 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 14659756 JRNL DOI 10.1016/J.JMB.2003.10.034 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 558128.820 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.9 REMARK 3 NUMBER OF REFLECTIONS : 5856 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) : 0.260 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.700 REMARK 3 FREE R VALUE TEST SET COUNT : 331 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.016 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 52.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 521 REMARK 3 BIN R VALUE (WORKING SET) : 0.3430 REMARK 3 BIN FREE R VALUE : 0.3570 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 33 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.062 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1315 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.81000 REMARK 3 B22 (A**2) : 10.17000 REMARK 3 B33 (A**2) : -20.98000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.38 REMARK 3 ESD FROM SIGMAA (A) : 0.41 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) : 0.55 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.50 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.320 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) : 1.700 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.020 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.010 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.250 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 38.56 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 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1P7N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000019109. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 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) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6743 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.2 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 51.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32900 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1EM9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MM HEPES-SODIUM BUFFER AND 0.8M REMARK 280 POTASSIUM SODIUM TARTRATE TETRAHYDRATE, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 85.19500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.93500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.93500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 42.59750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.93500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.93500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 127.79250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.93500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.93500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 42.59750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.93500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.93500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 127.79250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 85.19500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 -1.000000 0.000000 95.74000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 95.74000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 85.19500 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 PRO A -27 102.97 -51.72 REMARK 500 PRO A -24 -70.40 -59.46 REMARK 500 GLU A -11 -75.30 -54.48 REMARK 500 LEU A -10 -39.75 -35.27 REMARK 500 SER A -8 24.24 -65.70 REMARK 500 PRO A -4 -91.41 -16.76 REMARK 500 VAL A -2 -143.10 -167.40 REMARK 500 ALA A -1 68.61 -68.60 REMARK 500 LYS A 5 53.46 70.39 REMARK 500 ARG A 27 -78.92 -63.42 REMARK 500 THR A 28 -86.76 -48.67 REMARK 500 LYS A 29 -13.21 -44.18 REMARK 500 LEU A 31 -41.87 -130.27 REMARK 500 GLU A 99 48.33 -62.75 REMARK 500 THR A 101 172.42 -54.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EM9 RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITHOUT THE UPSTREAM EXTENSION REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PROTEIN SEQUENCE CONTAINS THE N-TERMINAL DOMAIN REMARK 999 OF CAPSID PROTEIN P27 WITH AN UPSTREAM 25-AMINO ACID REMARK 999 EXTENSION C-TERMINAL OF GAG P10 PROTEIN. DBREF 1P7N A -24 147 UNP P03322 GAG_RSVP 215 386 SEQADV 1P7N GLY A -28 UNP P03322 CLONING ARTIFACT SEQADV 1P7N PRO A -27 UNP P03322 CLONING ARTIFACT SEQADV 1P7N THR A -26 UNP P03322 CLONING ARTIFACT SEQADV 1P7N SER A -25 UNP P03322 CLONING ARTIFACT SEQRES 1 A 176 GLY PRO THR SER PRO GLY PRO ALA LEU THR ASP TRP ALA SEQRES 2 A 176 ARG VAL ARG GLU GLU LEU ALA SER THR GLY PRO PRO VAL SEQRES 3 A 176 VAL ALA MET PRO VAL VAL ILE LYS THR GLU GLY PRO ALA SEQRES 4 A 176 TRP THR PRO LEU GLU PRO LYS LEU ILE THR ARG LEU ALA SEQRES 5 A 176 ASP THR VAL ARG THR LYS GLY LEU ARG SER PRO ILE THR SEQRES 6 A 176 MET ALA GLU VAL GLU ALA LEU MET SER SER PRO LEU LEU SEQRES 7 A 176 PRO HIS ASP VAL THR ASN LEU MET ARG VAL ILE LEU GLY SEQRES 8 A 176 PRO ALA PRO TYR ALA LEU TRP MET ASP ALA TRP GLY VAL SEQRES 9 A 176 GLN LEU GLN THR VAL ILE ALA ALA ALA THR ARG ASP PRO SEQRES 10 A 176 ARG HIS PRO ALA ASN GLY GLN GLY ARG GLY GLU ARG THR SEQRES 11 A 176 ASN LEU ASN ARG LEU LYS GLY LEU ALA ASP GLY MET VAL SEQRES 12 A 176 GLY ASN PRO GLN GLY GLN ALA ALA LEU LEU ARG PRO GLY SEQRES 13 A 176 GLU LEU VAL ALA ILE THR ALA SER ALA LEU GLN ALA PHE SEQRES 14 A 176 ARG GLU VAL ALA ARG LEU ALA HELIX 1 1 ASP A -18 SER A -8 1 11 HELIX 2 2 GLU A 15 THR A 28 1 14 HELIX 3 3 SER A 33 MET A 44 1 12 HELIX 4 4 LEU A 49 GLY A 62 1 14 HELIX 5 5 GLY A 62 ASP A 87 1 26 HELIX 6 6 ASN A 102 LYS A 107 1 6 HELIX 7 7 ASN A 116 LEU A 124 1 9 HELIX 8 8 ARG A 125 LEU A 146 1 22 CRYST1 47.870 47.870 170.390 90.00 90.00 90.00 P 41 21 2 8 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 0.020890 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020890 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005869 0.00000