HEADER VIRAL PROTEIN 31-OCT-17 6BHR TITLE HIV-1 IMMATURE CTD-SP1 HEXAMER IN COMPLEX WITH IP6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN P24,SPACER PEPTIDE 1; COMPND 3 CHAIN: G; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SOURCE 3 SUBTYPE B (ISOLATE BH10); SOURCE 4 ORGANISM_TAXID: 11678; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ASSEMBLY, CO-FACTOR, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.ZADROZNY,J.M.WAGNER,B.K.GANSER-PORNILLOS,O.PORNILLOS REVDAT 7 04-OCT-23 6BHR 1 REMARK REVDAT 6 14-OCT-20 6BHR 1 HETSYN REVDAT 5 11-DEC-19 6BHR 1 REMARK REVDAT 4 20-FEB-19 6BHR 1 REMARK REVDAT 3 05-SEP-18 6BHR 1 JRNL REVDAT 2 15-AUG-18 6BHR 1 JRNL REVDAT 1 08-AUG-18 6BHR 0 JRNL AUTH R.A.DICK,K.K.ZADROZNY,C.XU,F.K.M.SCHUR,T.D.LYDDON, JRNL AUTH 2 C.L.RICANA,J.M.WAGNER,J.R.PERILLA,B.K.GANSER-PORNILLOS, JRNL AUTH 3 M.C.JOHNSON,O.PORNILLOS,V.M.VOGT JRNL TITL INOSITOL PHOSPHATES ARE ASSEMBLY CO-FACTORS FOR HIV-1. JRNL REF NATURE V. 560 509 2018 JRNL REFN ESSN 1476-4687 JRNL PMID 30069050 JRNL DOI 10.1038/S41586-018-0396-4 REMARK 2 REMARK 2 RESOLUTION. 2.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 76.8 REMARK 3 NUMBER OF REFLECTIONS : 2115 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.100 REMARK 3 FREE R VALUE TEST SET COUNT : 129 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.840 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 715 REMARK 3 ANGLE : 1.090 982 REMARK 3 CHIRALITY : 0.831 113 REMARK 3 PLANARITY : 0.004 121 REMARK 3 DIHEDRAL : 11.106 434 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'G' AND (RESID 280 THROUGH 306 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.7976 -15.9015 -3.0848 REMARK 3 T TENSOR REMARK 3 T11: -0.0113 T22: -0.0697 REMARK 3 T33: 0.3524 T12: -0.2841 REMARK 3 T13: 0.0189 T23: 0.0789 REMARK 3 L TENSOR REMARK 3 L11: 0.0463 L22: 0.0764 REMARK 3 L33: 0.1656 L12: -0.0376 REMARK 3 L13: 0.0155 L23: 0.0067 REMARK 3 S TENSOR REMARK 3 S11: -0.1553 S12: -0.0184 S13: -0.0878 REMARK 3 S21: -0.1729 S22: 0.0315 S23: -0.0573 REMARK 3 S31: 0.0865 S32: -0.0389 S33: -0.1345 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'G' AND (RESID 307 THROUGH 337 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.9965 -22.2326 1.5152 REMARK 3 T TENSOR REMARK 3 T11: 0.2563 T22: -0.1314 REMARK 3 T33: -0.0455 T12: -0.1377 REMARK 3 T13: -0.0003 T23: 0.3555 REMARK 3 L TENSOR REMARK 3 L11: 0.0119 L22: 0.0079 REMARK 3 L33: 0.0162 L12: -0.0051 REMARK 3 L13: -0.0095 L23: -0.0047 REMARK 3 S TENSOR REMARK 3 S11: -0.0928 S12: -0.0528 S13: -0.1084 REMARK 3 S21: -0.1793 S22: -0.0511 S23: 0.1075 REMARK 3 S31: 0.1780 S32: -0.0309 S33: -0.2649 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'G' AND (RESID 338 THROUGH 354 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.0560 -11.8531 7.1936 REMARK 3 T TENSOR REMARK 3 T11: 0.3190 T22: 0.3328 REMARK 3 T33: 0.1479 T12: 0.1180 REMARK 3 T13: 0.0681 T23: 0.1198 REMARK 3 L TENSOR REMARK 3 L11: 0.0319 L22: 0.0380 REMARK 3 L33: 0.0085 L12: 0.0283 REMARK 3 L13: -0.0028 L23: 0.0151 REMARK 3 S TENSOR REMARK 3 S11: -0.0210 S12: 0.0402 S13: -0.0307 REMARK 3 S21: -0.1299 S22: 0.1327 S23: 0.1076 REMARK 3 S31: -0.0958 S32: -0.0510 S33: 0.0060 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'G' AND (RESID 355 THROUGH 370 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.9327 -6.1931 20.9050 REMARK 3 T TENSOR REMARK 3 T11: 0.3038 T22: 0.3641 REMARK 3 T33: 0.1570 T12: 0.0233 REMARK 3 T13: 0.0676 T23: 0.0751 REMARK 3 L TENSOR REMARK 3 L11: 0.0225 L22: 0.0751 REMARK 3 L33: 0.2512 L12: -0.0143 REMARK 3 L13: 0.0544 L23: -0.1272 REMARK 3 S TENSOR REMARK 3 S11: -0.0224 S12: -0.0518 S13: 0.0408 REMARK 3 S21: 0.0508 S22: -0.0512 S23: 0.0217 REMARK 3 S31: 0.0432 S32: 0.0041 S33: -0.1105 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6BHR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1000230520. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2665 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5I4T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NACL 20% PEG 3350 0.1 M BIS-TRIS REMARK 280 PH 5.35, VAPOR DIFFUSION, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -167.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 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 G 278 REMARK 465 PRO G 279 REMARK 465 THR G 371 REMARK 465 ASN G 372 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 THR G 280 OG1 CG2 REMARK 470 ASP G 284 CG OD1 OD2 REMARK 470 LYS G 302 CG CD CE NZ REMARK 470 GLN G 311 CG CD OE1 NE2 REMARK 470 LYS G 335 CG CD CE NZ REMARK 470 GLU G 344 CG CD OE1 OE2 REMARK 470 ARG G 361 CG CD NE CZ NH1 NH2 REMARK 470 GLU G 365 CG CD OE1 OE2 REMARK 470 SER G 368 OG REMARK 470 VAL G 370 CG1 CG2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IHP G 401 DBREF 6BHR G 278 372 UNP P03347 GAG_HV1B1 278 372 SEQRES 1 G 95 SER PRO THR SER ILE LEU ASP ILE ARG GLN GLY PRO LYS SEQRES 2 G 95 GLU PRO PHE ARG ASP TYR VAL ASP ARG PHE TYR LYS THR SEQRES 3 G 95 LEU ARG ALA GLU GLN ALA SER GLN GLU VAL LYS ASN TRP SEQRES 4 G 95 MET THR GLU THR LEU LEU VAL GLN ASN ALA ASN PRO ASP SEQRES 5 G 95 CYS LYS THR ILE LEU LYS ALA LEU GLY PRO ALA ALA THR SEQRES 6 G 95 LEU GLU GLU MET MET THR ALA CYS GLN GLY VAL GLY GLY SEQRES 7 G 95 PRO GLY HIS LYS ALA ARG VAL LEU ALA GLU ALA MET SER SEQRES 8 G 95 GLN VAL THR ASN HET IHP G 401 36 HETNAM IHP INOSITOL HEXAKISPHOSPHATE HETSYN IHP MYO-INOSITOL HEXAKISPHOSPHATE; INOSITOL 1,2,3,4,5,6- HETSYN 2 IHP HEXAKISPHOSPHATE FORMUL 2 IHP C6 H18 O24 P6 FORMUL 3 HOH *(H2 O) HELIX 1 AA1 PRO G 292 ARG G 305 1 14 HELIX 2 AA2 SER G 310 ASN G 325 1 16 HELIX 3 AA3 ASN G 327 GLY G 338 1 12 HELIX 4 AA4 THR G 342 GLN G 351 1 10 HELIX 5 AA5 GLY G 355 VAL G 370 1 16 SITE 1 AC1 2 LYS G 290 LYS G 359 CRYST1 70.939 70.939 42.041 90.00 90.00 120.00 P 6 6 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 0.014097 0.008139 0.000000 0.00000 SCALE2 0.000000 0.016277 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023786 0.00000