HEADER CAPSID 20-JUN-97 1AM3 OBSLTE 14-OCT-98 1AM3 1A8O TITLE HIV CAPSID C-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV CAPSID; COMPND 3 CHAIN: NULL; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, RESIDUES 151 - 231; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 6 EXPRESSION_SYSTEM_VECTOR: PET11A; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: WISP97-7 KEYWDS CORE PROTEIN, HIV, CAPSID, C-TERMINAL DOMAIN EXPDTA X-RAY DIFFRACTION AUTHOR C.P.HILL,T.R.GAMBLE,S.YOO,F.F.VAJDOS,U.K.VON SCHWEDLER, AUTHOR 2 J.P.MCCUTCHEON,W.I.SUNDQUIST REVDAT 2 24-JUN-98 1AM3 3 REMARK CRYST1 SCALE REVDAT 1 14-JAN-98 1AM3 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, JRNL AUTH 3 C.P.HILL JRNL TITL STRUCTURE OF THE CARBOXYL-TERMINAL DIMERIZATION JRNL TITL 2 DOMAIN OF THE HIV-1 CAPSID PROTEIN JRNL REF SCIENCE V. 278 849 1997 JRNL REFN ASTM SCIEAS US ISSN 0036-8075 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 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) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 9029 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) : 0.229 REMARK 3 FREE R VALUE : 0.274 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 : 63 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 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) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.26 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) : 0.960 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.630 ; 3.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.770 ; 3.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.910 ; 5.000 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 1AM3 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : DEC-1996 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.40 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : 1-5 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.24 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : COLLIMATOR 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 : 9307 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.23200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: STRUCTURE DETERMINATION WAS DONE BY MAD USING DATA REMARK 200 COLLECTED AT BNL (X12C). REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,1/2+Z REMARK 290 3555 1/2-Y,1/2+X,3/4+Z REMARK 290 4555 1/2+Y,1/2-X,1/4+Z REMARK 290 5555 1/2-X,1/2+Y,3/4-Z REMARK 290 6555 1/2+X,1/2-Y,1/4-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,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 44.42000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.99000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.99000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 66.63000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.99000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.99000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.21000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.99000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.99000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 66.63000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.99000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.99000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.21000 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 44.42000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH 1031 LIES ON A SPECIAL POSITION. 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 N ALA 27 O HOH 1035 6565 1.53 REMARK 500 O HOH 1047 O HOH 1049 6465 1.55 REMARK 500 O HOH 1035 O HOH 1036 6465 1.69 REMARK 500 O HOH 1060 O HOH 1061 6465 1.85 REMARK 500 NZ LYS 32 O ALA 54 6565 1.95 REMARK 500 O HOH 1000 O HOH 1015 3654 2.13 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET 1 SD MET 1 CE 0.060 REMARK 500 MET 64 CG MET 64 SD 0.047 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 1007 DISTANCE = 5.53 ANGSTROMS REMARK 525 HOH 1035 DISTANCE = 5.73 ANGSTROMS REMARK 860 REMARK 860 CORRECTION AFTER RELEASE REMARK 860 CORRECT CELL DIMENSIONS BASED ON INFORMATION FROM THE REMARK 860 DEPOSITOR AND MAKE RELATED CHANGES. ADD INFORMATION TO REMARK 860 REMARK 3. 24-JUN-1998. REMARK 999 REMARK 999 SEQUENCE REMARK 999 1AM3 SWS P12493 1 - 281 NOT IN ATOMS LIST REMARK 999 1AM3 SWS P12493 352 - 499 NOT IN ATOMS LIST DBREF 1AM3 1 70 UNP P12493 GAG_HV1N5 282 351 SEQADV 1AM3 MET 1 UNP P12493 LEU 282 CONFLICT SEQRES 1 70 MET ASP ILE ARG GLN GLY PRO LYS GLU PRO PHE ARG ASP SEQRES 2 70 TYR VAL ASP ARG PHE TYR LYS THR LEU ARG ALA GLU GLN SEQRES 3 70 ALA SER GLN GLU VAL LYS ASN TRP MET THR GLU THR LEU SEQRES 4 70 LEU VAL GLN ASN ALA ASN PRO ASP CYS LYS THR ILE LEU SEQRES 5 70 LYS ALA LEU GLY PRO GLY ALA THR LEU GLU GLU MET MET SEQRES 6 70 THR ALA CYS GLN GLY FORMUL 2 HOH *63(H2 O1) HELIX 1 1 PHE 11 GLU 25 1 15 HELIX 2 2 GLN 29 GLU 37 1 9 HELIX 3 3 LEU 39 GLN 42 1 4 HELIX 4 4 PRO 46 LEU 55 1 10 HELIX 5 5 LEU 61 ALA 67 1 7 SSBOND 1 CYS 48 CYS 68 CRYST1 41.980 41.980 88.840 90.00 90.00 90.00 P 43 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 0.023821 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023821 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011256 0.00000