10 20 30 40 50 60 70 80 1A43 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER VIRAL PROTEIN 10-FEB-98 1A43
TITLE STRUCTURE OF THE HIV-1 CAPSID PROTEIN DIMERIZATION DOMAIN TITLE 2 AT 2.6A RESOLUTION
COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 CAPSID; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN OF HIV-1 CAPSID PROTEIN COMPND 5 RESIDUES 146-231 (CAPSID NUMBERING); 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: BL21
KEYWDS CAPSID, ASSEMBLY PROTEIN, HIV-1, VIRAL PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR D.K.WORTHYLAKE,H.WANG,S.YOO,W.I.SUNDQUIST,C.P.HILL
REVDAT 3 24-FEB-09 1A43 1 VERSN REVDAT 2 01-APR-03 1A43 1 JRNL REVDAT 1 09-FEB-99 1A43 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 JRNL TITL 2 DIMERIZATION DOMAIN 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 1
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) (%) : 91.8 REMARK 3 NUMBER OF REFLECTIONS : 3102 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) : 0.223 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 303 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) (%) : 99.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 500 REMARK 3 BIN R VALUE (WORKING SET) : 0.3770 REMARK 3 BIN FREE R VALUE : 0.5210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 57 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.069 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 573 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 28 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 59.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.00 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) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.50 REMARK 3 LOW RESOLUTION CUTOFF (A) : 20.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.60 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.15 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) : 2.670 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.440 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.340 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.020 ; 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : TIP3P.PARAMETER REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TIP3P.TOPOLOGY REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
REMARK 4 REMARK 4 1A43 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
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 : 1 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 : MIRRORS 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 : 3102 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 (%) : NULL 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 : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.843 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 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 30.20500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 30.20500 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.21500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.20500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.10750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.20500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.32250 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.20500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.20500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 30.21500 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 30.20500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 45.32250 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 30.20500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 15.10750 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 60.41000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 60.41000 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 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 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 -83.55 -116.91 REMARK 500 REMARK 500 REMARK: NULL
DBREF 1A43 A 146 231 UNP P12497 POL_HV1N5 277 362
SEQRES 1 A 87 MET SER PRO THR SER ILE LEU ASP ILE ARG GLN GLY PRO SEQRES 2 A 87 LYS GLU PRO PHE ARG ASP TYR VAL ASP ARG PHE TYR LYS SEQRES 3 A 87 THR LEU ARG ALA GLU GLN ALA SER GLN GLU VAL LYS ASN SEQRES 4 A 87 TRP MET THR GLU THR LEU LEU VAL GLN ASN ALA ASN PRO SEQRES 5 A 87 ASP CYS LYS THR ILE LEU LYS ALA LEU GLY PRO GLY ALA SEQRES 6 A 87 THR LEU GLU GLU MET MET THR ALA CYS GLN GLY VAL GLY SEQRES 7 A 87 GLY PRO GLY HIS LYS ALA ARG VAL LEU
FORMUL 2 HOH *28(H2 O)
HELIX 1 1 ILE A 150 ASP A 152 5 3 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 ALA A 217 1 7
SSBOND 1 CYS A 198 CYS A 218 1555 1555 2.04
CRYST1 60.410 60.410 60.430 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 0.016554 0.000000 0.000000 0.00000
SCALE2 0.000000 0.016554 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016548 0.00000