PDB Short entry for 1BAJ HEADER VIRAL PROTEIN 17-APR-98 1BAJ TITLE HIV-1 CAPSID PROTEIN C-TERMINAL FRAGMENT PLUS GAG P2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN OF HIV-1 CAPSID PROTEIN (RESIDUES 146-229 COMPND 5 CAPSID NUMBERING) FOLLOWED BY THE 14 AMINO ACID P2 DOMAIN OF GAG; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 CELL_LINE: BL21; SOURCE 5 GENE: GAG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: BL21; SOURCE 10 EXPRESSION_SYSTEM_GENE: GAG KEYWDS CAPSID, HIV-1 ASSEMBLY PROTEIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.K.WORTHYLAKE,H.WANG,S.YOO,W.I.SUNDQUIST,C.P.HILL REVDAT 5 02-AUG-23 1BAJ 1 SEQADV REVDAT 4 24-FEB-09 1BAJ 1 VERSN REVDAT 3 01-APR-03 1BAJ 1 JRNL REVDAT 2 18-NOV-98 1BAJ 3 ATOM SOURCE REMARK HETATM REVDAT 2 2 3 KEYWDS REVDAT 1 14-OCT-98 1BAJ 0 JRNL AUTH D.K.WORTHYLAKE,H.WANG,S.YOO,W.I.SUNDQUIST,C.P.HILL JRNL TITL STRUCTURES OF THE HIV-1 CAPSID PROTEIN DIMERIZATION DOMAIN JRNL TITL 2 AT 2.6 A RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 55 85 1999 JRNL REFN ISSN 0907-4449 JRNL PMID 10089398 JRNL DOI 10.1107/S0907444998007689 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 3200 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) : 0.207 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.900 REMARK 3 FREE R VALUE TEST SET COUNT : 349 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.015 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) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 519 REMARK 3 BIN R VALUE (WORKING SET) : 0.3620 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 53 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.041 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 563 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 27 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.41 REMARK 3 LOW RESOLUTION CUTOFF (A) : 20.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.38 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.230 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) : 3.610 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.910 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.510 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 10.740; 2.500 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1BAJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171528. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : SEP-97 REMARK 200 TEMPERATURE (KELVIN) : 300 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3227 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 <I/SIGMA(I)> FOR SHELL : 7.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1AM3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 30.66500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 30.66500 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.78500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.66500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 14.89250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.66500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 44.67750 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.66500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.66500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 29.78500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 30.66500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 44.67750 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 30.66500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 14.89250 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 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 -1.000000 0.000000 0.000000 61.33000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 61.33000 REMARK 350 BIOMT3 2 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 145 REMARK 465 SER A 146 REMARK 465 PRO A 147 REMARK 465 GLN A 219 REMARK 465 GLY A 220 REMARK 465 VAL A 221 REMARK 465 GLY A 222 REMARK 465 GLY A 223 REMARK 465 PRO A 224 REMARK 465 GLY A 225 REMARK 465 HIS A 226 REMARK 465 LYS A 227 REMARK 465 ALA A 228 REMARK 465 ARG A 229 REMARK 465 VAL A 230 REMARK 465 LEU A 231 REMARK 465 ALA A 232 REMARK 465 GLU A 233 REMARK 465 ALA A 234 REMARK 465 MET A 235 REMARK 465 SER A 236 REMARK 465 GLN A 237 REMARK 465 VAL A 238 REMARK 465 THR A 239 REMARK 465 ASN A 240 REMARK 465 PRO A 241 REMARK 465 ALA A 242 REMARK 465 THR A 243 REMARK 465 ILE A 244 REMARK 465 MET A 245 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 THR A 188 -87.14 -126.98 REMARK 500 REMARK 500 REMARK: NULL DBREF 1BAJ A 145 245 UNP P12497 POL_HV1N5 275 376 SEQADV 1BAJ MET A 145 UNP P12497 TYR 276 CONFLICT SEQRES 1 A 101 MET SER PRO THR SER ILE LEU ASP ILE ARG GLN GLY PRO SEQRES 2 A 101 LYS GLU PRO PHE ARG ASP TYR VAL ASP ARG PHE TYR LYS SEQRES 3 A 101 THR LEU ARG ALA GLU GLN ALA SER GLN GLU VAL LYS ASN SEQRES 4 A 101 TRP MET THR GLU THR LEU LEU VAL GLN ASN ALA ASN PRO SEQRES 5 A 101 ASP CYS LYS THR ILE LEU LYS ALA LEU GLY PRO GLY ALA SEQRES 6 A 101 THR LEU GLU GLU MET MET THR ALA CYS GLN GLY VAL GLY SEQRES 7 A 101 GLY PRO GLY HIS LYS ALA ARG VAL LEU ALA GLU ALA MET SEQRES 8 A 101 SER GLN VAL THR ASN PRO ALA THR ILE MET FORMUL 2 HOH *27(H2 O) HELIX 1 1 SER A 149 ASP A 152 5 4 HELIX 2 2 PHE A 161 ALA A 174 1 14 HELIX 3 3 GLN A 179 GLU A 187 1 9 HELIX 4 4 LEU A 189 GLN A 192 1 4 HELIX 5 5 PRO A 196 LEU A 205 1 10 HELIX 6 6 LEU A 211 THR A 216 1 6 SSBOND 1 CYS A 198 CYS A 218 1555 1555 2.04 CRYST1 61.330 61.330 59.570 90.00 90.00 90.00 I 41 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 0.016305 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016305 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016787 0.00000