HEADER STRUCTURAL PROTEIN 29-JAN-14 4COP TITLE HIV-1 CAPSID C-TERMINAL DOMAIN MUTANT (Y169S) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN P24; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, RESIDUES 278-363; COMPND 5 SYNONYM: PR160GAG-POL, GAG POLYPROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11676; SOURCE 5 STRAIN: NL4-3; SOURCE 6 ATCC: 11698; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VARIANT: CODONPLUS-RIL; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_VECTOR: PET11C KEYWDS STRUCTURAL PROTEIN, HUMAN IMMUNODEFICIENCY VIRUS, VIRUS ASSEMBLY, KEYWDS 2 HELICAL RECONSTRUCTION, CAPSID EXPDTA X-RAY DIFFRACTION AUTHOR T.A.M.BHARAT,L.R.CASTILLO-MENENDEZ,W.J.H.HAGEN,V.LUX,S.IGONET, AUTHOR 2 M.SCHORB,F.K.M.SCHUR,H.-G.KRAUSSLICH,J.A.G.BRIGGS REVDAT 5 20-DEC-23 4COP 1 REMARK REVDAT 4 13-NOV-19 4COP 1 REMARK REVDAT 3 27-AUG-14 4COP 1 REMARK REVDAT 2 25-JUN-14 4COP 1 JRNL REVDAT 1 04-JUN-14 4COP 0 JRNL AUTH T.A.M.BHARAT,L.R.CASTILLO MENENDEZ,W.J.H.HAGEN,V.LUX, JRNL AUTH 2 S.IGONET,M.SCHORB,F.K.M.SCHUR,H.KRAUSSLICH,J.A.G.BRIGGS JRNL TITL CRYO-ELECTRON MICROSCOPY OF TUBULAR ARRAYS OF HIV-1 GAG JRNL TITL 2 RESOLVES STRUCTURES ESSENTIAL FOR IMMATURE VIRUS ASSEMBLY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 8233 2014 JRNL REFN ISSN 0027-8424 JRNL PMID 24843179 JRNL DOI 10.1073/PNAS.1401455111 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.4 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 3 NUMBER OF REFLECTIONS : 12050 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 + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 594 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 : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.03 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.57 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2340 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.3391 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2220 REMARK 3 BIN R VALUE (WORKING SET) : 0.3376 REMARK 3 BIN FREE R VALUE : 0.3630 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.13 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 120 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 : 1186 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 124 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.65610 REMARK 3 B22 (A**2) : 4.46490 REMARK 3 B33 (A**2) : -3.80880 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.96690 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.319 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.207 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.158 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.199 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.156 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.918 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1221 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1648 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 449 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 36 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 172 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1221 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 164 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1515 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 0.90 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 1.74 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.41 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4COP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1290059634. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 10.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : HORIZONTALLY SIDE DIFFRACTING REMARK 200 SILICON 111 CRYSTAL REMARK 200 OPTICS : ONE PAIR OF (300X40X15) MM3 LONG REMARK 200 PT COATED SI MIRROR, 260MM REMARK 200 USABLE, IN A KIRKPATRICK-BAEZ REMARK 200 GEOMETRY REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12273 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 36.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2BUO REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M NAH2PO4, 0.8 M K2HPO4, 0.1 M REMARK 280 CAPS PH 10.5 AND 0.2 M LISO4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 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 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 36.19500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 REMARK 350 TOTAL BURIED SURFACE AREA: 980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 SER A 146 REMARK 465 SER B 146 REMARK 465 PRO B 147 REMARK 465 THR B 148 REMARK 465 GLY B 206 REMARK 465 PRO B 207 REMARK 465 GLY B 208 REMARK 465 GLY B 220 REMARK 465 VAL B 221 REMARK 465 GLY B 222 REMARK 465 GLY B 223 REMARK 465 PRO B 224 REMARK 465 GLY B 225 REMARK 465 HIS B 226 REMARK 465 LYS B 227 REMARK 465 ALA B 228 REMARK 465 ARG B 229 REMARK 465 VAL B 230 REMARK 465 LEU B 231 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PRO A 147 N CB CG CD REMARK 470 LEU A 231 CA C O CB CG CD1 CD2 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 -73.03 -97.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4COC RELATED DB: PDB REMARK 900 HIV-1 CAPSID C-TERMINAL DOMAIN MUTANT (Y169L) REMARK 900 RELATED ID: EMD-2638 RELATED DB: EMDB DBREF 4COP A 146 231 UNP P12497 POL_HV1N5 278 363 DBREF 4COP B 146 231 UNP P12497 POL_HV1N5 278 363 SEQADV 4COP SER A 169 UNP P12497 TYR 301 ENGINEERED MUTATION SEQADV 4COP SER B 169 UNP P12497 TYR 301 ENGINEERED MUTATION SEQRES 1 A 86 SER PRO THR SER ILE LEU ASP ILE ARG GLN GLY PRO LYS SEQRES 2 A 86 GLU PRO PHE ARG ASP TYR VAL ASP ARG PHE SER LYS THR SEQRES 3 A 86 LEU ARG ALA GLU GLN ALA SER GLN GLU VAL LYS ASN TRP SEQRES 4 A 86 MET THR GLU THR LEU LEU VAL GLN ASN ALA ASN PRO ASP SEQRES 5 A 86 CYS LYS THR ILE LEU LYS ALA LEU GLY PRO GLY ALA THR SEQRES 6 A 86 LEU GLU GLU MET MET THR ALA CYS GLN GLY VAL GLY GLY SEQRES 7 A 86 PRO GLY HIS LYS ALA ARG VAL LEU SEQRES 1 B 86 SER PRO THR SER ILE LEU ASP ILE ARG GLN GLY PRO LYS SEQRES 2 B 86 GLU PRO PHE ARG ASP TYR VAL ASP ARG PHE SER LYS THR SEQRES 3 B 86 LEU ARG ALA GLU GLN ALA SER GLN GLU VAL LYS ASN TRP SEQRES 4 B 86 MET THR GLU THR LEU LEU VAL GLN ASN ALA ASN PRO ASP SEQRES 5 B 86 CYS LYS THR ILE LEU LYS ALA LEU GLY PRO GLY ALA THR SEQRES 6 B 86 LEU GLU GLU MET MET THR ALA CYS GLN GLY VAL GLY GLY SEQRES 7 B 86 PRO GLY HIS LYS ALA ARG VAL LEU FORMUL 3 HOH *124(H2 O) HELIX 1 1 SER A 149 ILE A 153 5 5 HELIX 2 2 PRO A 160 GLU A 175 1 16 HELIX 3 3 SER A 178 ASN A 193 1 16 HELIX 4 4 ASN A 195 GLY A 206 1 12 HELIX 5 5 THR A 210 GLN A 219 1 10 HELIX 6 6 SER B 149 ILE B 153 5 5 HELIX 7 7 PRO B 160 GLU B 175 1 16 HELIX 8 8 SER B 178 ASN B 193 1 16 HELIX 9 9 ASN B 195 LEU B 205 1 11 HELIX 10 10 THR B 210 GLN B 219 1 10 CRYST1 32.560 72.390 35.700 90.00 109.32 90.00 P 1 21 1 4 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 0.030713 0.000000 0.010767 0.00000 SCALE2 0.000000 0.013814 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029683 0.00000