HEADER VIRAL PROTEIN 24-JUL-13 3WFV TITLE HIV-1 CRF07 GP41 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN GP160; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 542-577 AND 624-660; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: ENV; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET30 KEYWDS DOUBLE HELIX, ALPHA-HELIX, VIRUS FUSION, GLYCOPROTEIN, MEMBRANE, KEYWDS 2 VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.DU,H.XUE,J.MA,F.LIU,J.ZHOU,Y.SHAO,W.QIAO,X.LIU REVDAT 3 20-MAR-24 3WFV 1 SEQADV REVDAT 2 16-AUG-17 3WFV 1 SOURCE REMARK REVDAT 1 16-OCT-13 3WFV 0 JRNL AUTH J.DU,H.XUE,J.MA,F.LIU,J.ZHOU,Y.SHAO,W.QIAO,X.LIU JRNL TITL THE CRYSTAL STRUCTURE OF HIV CRF07 B'/C GP41 REVEALS A JRNL TITL 2 HYPER-MUTANT SITE IN THE MIDDLE OF HR2 HEPTAD REPEAT JRNL REF VIROLOGY V. 446 86 2013 JRNL REFN ISSN 0042-6822 JRNL PMID 24074570 JRNL DOI 10.1016/J.VIROL.2013.07.024 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 7326 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.590 REMARK 3 FREE R VALUE TEST SET COUNT : 336 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 20.1036 - 2.2674 0.96 3573 161 0.2192 0.2473 REMARK 3 2 2.2674 - 1.8000 0.96 3417 175 0.2233 0.2960 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 : 0.48 REMARK 3 B_SOL : 87.43 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.80600 REMARK 3 B22 (A**2) : -2.80600 REMARK 3 B33 (A**2) : 5.61200 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 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 : 0.008 693 REMARK 3 ANGLE : 1.226 935 REMARK 3 CHIRALITY : 0.084 102 REMARK 3 PLANARITY : 0.004 124 REMARK 3 DIHEDRAL : 19.140 259 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3WFV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000096283. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7326 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.102 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 11.40 REMARK 200 R MERGE FOR SHELL (I) : 0.12500 REMARK 200 R SYM FOR SHELL (I) : 0.05300 REMARK 200 FOR SHELL : 17.50 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG6000, 0.1M TRIS, 40% MPD, PH REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 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 SMTRY1 7 1.000000 0.000000 0.000000 23.46000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 13.54464 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 61.68367 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 23.46000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 13.54464 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 61.68367 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 23.46000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 13.54464 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 61.68367 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 23.46000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 13.54464 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 61.68367 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 23.46000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 13.54464 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 61.68367 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 23.46000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 13.54464 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 61.68367 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 27.08927 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 123.36733 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 27.08927 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 123.36733 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 27.08927 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 123.36733 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 27.08927 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 123.36733 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 27.08927 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 123.36733 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 27.08927 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 123.36733 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 KCAL/MOL 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 -0.500000 -0.866025 0.000000 23.46000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 40.63391 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -23.46000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 40.63391 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 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 A 701 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 702 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 730 LIES ON A SPECIAL POSITION. 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 OE2 GLU A 560 O HOH A 711 2.02 REMARK 500 REMARK 500 REMARK: NULL DBREF 3WFV A 546 581 UNP Q994K2 Q994K2_9HIV1 542 577 DBREF 3WFV A 587 623 UNP Q994K2 Q994K2_9HIV1 624 660 SEQADV 3WFV ALA A 538 UNP Q994K2 EXPRESSION TAG SEQADV 3WFV GLY A 539 UNP Q994K2 EXPRESSION TAG SEQADV 3WFV ALA A 540 UNP Q994K2 EXPRESSION TAG SEQADV 3WFV GLY A 541 UNP Q994K2 EXPRESSION TAG SEQADV 3WFV GLN A 542 UNP Q994K2 EXPRESSION TAG SEQADV 3WFV SER A 543 UNP Q994K2 EXPRESSION TAG SEQADV 3WFV ASN A 544 UNP Q994K2 EXPRESSION TAG SEQADV 3WFV ASP A 545 UNP Q994K2 EXPRESSION TAG SEQADV 3WFV GLY A 582 UNP Q994K2 LINKER SEQADV 3WFV GLY A 583 UNP Q994K2 LINKER SEQADV 3WFV GLY A 584 UNP Q994K2 LINKER SEQADV 3WFV GLY A 585 UNP Q994K2 LINKER SEQADV 3WFV ARG A 586 UNP Q994K2 LINKER SEQADV 3WFV VAL A 601 UNP Q994K2 ILE 638 CONFLICT SEQADV 3WFV ALA A 623 UNP Q994K2 ASP 660 CONFLICT SEQRES 1 A 86 ALA GLY ALA GLY GLN SER ASN ASP SER GLY ILE VAL GLN SEQRES 2 A 86 GLN GLN SER ASN LEU LEU ARG ALA ILE GLU ALA GLN GLN SEQRES 3 A 86 HIS LEU LEU GLN LEU THR VAL TRP GLY ILE LYS GLN LEU SEQRES 4 A 86 GLN THR ARG VAL LEU GLY GLY GLY GLY ARG TRP MET GLN SEQRES 5 A 86 TRP ASP LYS GLU ILE SER ASN TYR THR ASN THR VAL TYR SEQRES 6 A 86 ARG LEU LEU GLU GLU SER GLN ASN GLN GLN GLU ARG ASN SEQRES 7 A 86 GLU LYS ASP LEU LEU ALA LEU ALA FORMUL 2 HOH *30(H2 O) HELIX 1 1 ALA A 538 LEU A 581 1 44 HELIX 2 2 GLY A 585 ALA A 621 1 37 CISPEP 1 GLY A 582 GLY A 583 0 -17.27 CRYST1 46.920 46.920 185.051 90.00 90.00 120.00 H 3 2 18 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 0.021313 0.012305 0.000000 0.00000 SCALE2 0.000000 0.024610 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005404 0.00000