PDB Short entry for 1AUM HEADER VIRAL PROTEIN 29-AUG-97 1AUM TITLE HIV CAPSID C-TERMINAL DOMAIN (CAC146) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV CAPSID; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, RESIDUES 146 - 231; COMPND 5 SYNONYM: CAC146; 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_VECTOR: PET11A; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: WISP97-7 KEYWDS CORE PROTEIN, HIV, CAPSID, C-TERMINAL DOMAIN, CAC146, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.P.HILL,T.R.GAMBLE,S.YOO,F.F.VAJDOS,U.K.VON SCHWEDLER, AUTHOR 2 D.K.WORTHYLAKE,H.WANG,J.P.MCCUTCHEON,W.I.SUNDQUIST REVDAT 4 03-APR-24 1AUM 1 REMARK REVDAT 3 24-FEB-09 1AUM 1 VERSN REVDAT 2 01-APR-03 1AUM 1 JRNL REVDAT 1 14-JAN-98 1AUM 0 JRNL AUTH T.R.GAMBLE,S.YOO,F.F.VAJDOS,U.K.VON SCHWEDLER, JRNL AUTH 2 D.K.WORTHYLAKE,H.WANG,J.P.MCCUTCHEON,W.I.SUNDQUIST,C.P.HILL JRNL TITL STRUCTURE OF THE CARBOXYL-TERMINAL DIMERIZATION DOMAIN OF JRNL TITL 2 THE HIV-1 CAPSID PROTEIN. JRNL REF SCIENCE V. 278 849 1997 JRNL REFN ISSN 0036-8075 JRNL PMID 9346481 JRNL DOI 10.1126/SCIENCE.278.5339.849 REMARK 2 REMARK 2 RESOLUTION. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 2677 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.355 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 556 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) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.44 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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: NULL REMARK 4 REMARK 4 1AUM 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_1000171278. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUL-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2681 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 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) : 0.36800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.843 REMARK 200 STARTING MODEL: C-TERMINAL CAPSID (151 - 231) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS OF CAC(146-231) WERE GROWN AT REMARK 280 4C IN 8 MICROLITER SITTING DROPS CONTAINING A 1:1 MIXTURE OF REMARK 280 PROTEIN SOLUTION (2.1 MM CA(151-231) IN 10 MM TRIS (PH 8.0) AND REMARK 280 2 MM 2-MERCAPTOETHANOL) AND RESERVOIR SOLUTION (2.0 M AMMONIUM REMARK 280 SULFATE), VAPOR DIFFUSION - SITTING DROP, VAPOR DIFFUSION, REMARK 280 SITTING DROP 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 30.24000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 30.24000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.84500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.24000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 14.92250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.24000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 44.76750 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.24000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.24000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 29.84500 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 30.24000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 44.76750 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 30.24000 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 14.92250 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 60.48000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 60.48000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 170 CE NZ REMARK 480 GLN A 176 CB CG CD OE1 NE2 REMARK 480 LYS A 182 NZ REMARK 480 LYS A 199 CE NZ REMARK 480 LYS A 203 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 CD1 LEU A 151 CD1 LEU A 189 1.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CZ ARG A 162 HG1 THR A 200 7554 0.35 REMARK 500 HH12 ARG A 162 O PRO A 196 7554 0.43 REMARK 500 CZ ARG A 162 OG1 THR A 200 7554 0.78 REMARK 500 NE ARG A 162 OG1 THR A 200 7554 0.84 REMARK 500 NH1 ARG A 162 HG1 THR A 200 7554 1.04 REMARK 500 NH1 ARG A 162 O PRO A 196 7554 1.11 REMARK 500 HE ARG A 162 CB THR A 200 7554 1.13 REMARK 500 HE ARG A 162 CG2 THR A 200 7554 1.13 REMARK 500 HH22 ARG A 162 H THR A 200 7554 1.22 REMARK 500 NE ARG A 162 CB THR A 200 7554 1.30 REMARK 500 HE ARG A 162 OG1 THR A 200 7554 1.34 REMARK 500 HH22 ARG A 162 N THR A 200 7554 1.35 REMARK 500 HH21 ARG A 162 CA THR A 200 7554 1.37 REMARK 500 NH2 ARG A 162 H THR A 200 7554 1.44 REMARK 500 NH2 ARG A 162 N THR A 200 7554 1.46 REMARK 500 NE ARG A 162 HG1 THR A 200 7554 1.48 REMARK 500 NH2 ARG A 162 HG1 THR A 200 7554 1.55 REMARK 500 NH2 ARG A 162 OG1 THR A 200 7554 1.58 REMARK 500 CZ ARG A 162 CB THR A 200 7554 1.65 REMARK 500 NH2 ARG A 162 CA THR A 200 7554 1.72 REMARK 500 CG1 ILE A 201 CE MET A 215 8555 1.93 REMARK 500 NH2 ARG A 162 CB THR A 200 7554 1.96 REMARK 500 NH1 ARG A 162 OG1 THR A 200 7554 1.98 REMARK 500 NE ARG A 162 CG2 THR A 200 7554 1.99 REMARK 500 CG2 ILE A 201 OE2 GLU A 212 8555 2.07 REMARK 500 CD2 LEU A 189 OE1 GLN A 192 6665 2.15 REMARK 500 CD ARG A 162 OG1 THR A 200 7554 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 -88.34 -99.45 REMARK 500 REMARK 500 REMARK: NULL DBREF 1AUM A 151 220 UNP P12497 POL_HV1N5 282 351 SEQRES 1 A 70 LEU ASP ILE ARG GLN GLY PRO LYS GLU PRO PHE ARG ASP SEQRES 2 A 70 TYR VAL ASP ARG PHE TYR LYS THR LEU ARG ALA GLU GLN SEQRES 3 A 70 ALA SER GLN GLU VAL LYS ASN TRP MET THR GLU THR LEU SEQRES 4 A 70 LEU VAL GLN ASN ALA ASN PRO ASP CYS LYS THR ILE LEU SEQRES 5 A 70 LYS ALA LEU GLY PRO GLY ALA THR LEU GLU GLU MET MET SEQRES 6 A 70 THR ALA CYS GLN GLY HELIX 1 1 PHE A 161 GLU A 175 1 15 HELIX 2 2 GLN A 179 GLU A 187 1 9 HELIX 3 3 LEU A 189 GLN A 192 1 4 HELIX 4 4 PRO A 196 LEU A 205 1 10 HELIX 5 5 LEU A 211 ALA A 217 1 7 SSBOND 1 CYS A 198 CYS A 218 1555 1555 2.41 CRYST1 60.480 60.480 59.690 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 0.016534 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016534 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016753 0.00000