HEADER VIRAL PROTEIN 13-FEB-09 3G9R TITLE STRUCTURE OF THE HIV-1 GP41 MEMBRANE-PROXIMAL ECTODOMAIN REGION IN A TITLE 2 PUTATIVE PREFUSION CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: FUSION COMPLEX OF HIV-1 ENVELOPE GLYCOPROTEIN AND COMPND 3 SACCHAROMYCES CEREVISIAE GENERAL CONTROL PROTEIN GCN4; COMPND 4 CHAIN: A, B, C, D, E, F; COMPND 5 FRAGMENT: C-TERMINAL MPER OF HIV-1 GP41, LEUCINE-ZIPPER DOMAIN OF COMPND 6 GCN4; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1, SACCHAROMYCES SOURCE 3 CEREVISIAE; SOURCE 4 ORGANISM_TAXID: 11676, 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GP41, MPER, HIV-1, MEMBRANE FUSION, AIDS, APOPTOSIS, CELL MEMBRANE, KEYWDS 2 COILED COIL, ENVELOPE PROTEIN, FUSION PROTEIN, HOST-VIRUS KEYWDS 3 INTERACTION, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LIU,M.LU REVDAT 4 06-SEP-23 3G9R 1 REMARK REVDAT 3 20-OCT-21 3G9R 1 REMARK SEQADV REVDAT 2 02-AUG-17 3G9R 1 SOURCE REMARK REVDAT 1 12-MAY-09 3G9R 0 JRNL AUTH J.LIU,Y.DENG,A.DEY,J.MOORE,M.LU JRNL TITL STRUCTURE OF THE HIV-1 GP41 MEMBRANE-PROXIMAL ECTODOMAIN JRNL TITL 2 REGION IN A PUTATIVE PREFUSION CONFORMATION. JRNL REF BIOCHEMISTRY V. 48 2915 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19226163 JRNL DOI 10.1021/BI802303B REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 22010 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1110 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1472 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2241 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 89 REMARK 3 SOLVENT ATOMS : 78 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.93000 REMARK 3 B22 (A**2) : 2.96000 REMARK 3 B33 (A**2) : -4.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.58000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.202 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.187 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.155 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.784 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2383 ; 0.026 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3215 ; 2.029 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 238 ; 4.795 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 109 ;35.858 ;23.945 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 494 ;18.903 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;18.190 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 321 ; 0.139 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1646 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1029 ; 0.237 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1622 ; 0.327 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 72 ; 0.192 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 62 ; 0.287 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.289 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1277 ; 1.384 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1988 ; 2.125 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1418 ; 3.441 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1227 ; 4.446 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 42 REMARK 3 ORIGIN FOR THE GROUP (A): 6.7020 5.7160 13.5750 REMARK 3 T TENSOR REMARK 3 T11: -0.2518 T22: -0.1055 REMARK 3 T33: -0.1311 T12: -0.1103 REMARK 3 T13: 0.0318 T23: -0.0219 REMARK 3 L TENSOR REMARK 3 L11: 1.2163 L22: 3.6545 REMARK 3 L33: 30.8846 L12: -1.3924 REMARK 3 L13: 5.3354 L23: -8.5612 REMARK 3 S TENSOR REMARK 3 S11: -0.0389 S12: 0.0008 S13: 0.1121 REMARK 3 S21: 0.2350 S22: -0.2357 S23: -0.1787 REMARK 3 S31: -0.7576 S32: 1.0979 S33: 0.2746 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 42 REMARK 3 ORIGIN FOR THE GROUP (A): -0.5610 -1.7450 13.4520 REMARK 3 T TENSOR REMARK 3 T11: -0.3234 T22: -0.2293 REMARK 3 T33: -0.0916 T12: 0.0773 REMARK 3 T13: -0.0346 T23: -0.0493 REMARK 3 L TENSOR REMARK 3 L11: 1.2232 L22: 1.4639 REMARK 3 L33: 31.2792 L12: 0.1125 REMARK 3 L13: 3.9663 L23: -4.2753 REMARK 3 S TENSOR REMARK 3 S11: -0.0282 S12: -0.1144 S13: -0.0644 REMARK 3 S21: 0.0462 S22: 0.0362 S23: 0.0672 REMARK 3 S31: -0.1952 S32: 0.0830 S33: -0.0080 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 3 C 42 REMARK 3 ORIGIN FOR THE GROUP (A): 9.5200 -4.3670 11.8430 REMARK 3 T TENSOR REMARK 3 T11: -0.1186 T22: -0.0802 REMARK 3 T33: -0.1199 T12: 0.1580 REMARK 3 T13: -0.0412 T23: -0.1367 REMARK 3 L TENSOR REMARK 3 L11: 1.5283 L22: 3.1648 REMARK 3 L33: 23.5851 L12: 0.1305 REMARK 3 L13: -0.2220 L23: -8.0912 REMARK 3 S TENSOR REMARK 3 S11: -0.0664 S12: 0.0820 S13: -0.1865 REMARK 3 S21: 0.0521 S22: 0.2583 S23: 0.0510 REMARK 3 S31: 0.7165 S32: 0.1741 S33: -0.1919 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 2 D 42 REMARK 3 ORIGIN FOR THE GROUP (A): -20.6000 11.7060 12.3030 REMARK 3 T TENSOR REMARK 3 T11: -0.2239 T22: -0.0971 REMARK 3 T33: -0.1320 T12: 0.1134 REMARK 3 T13: -0.0045 T23: 0.0285 REMARK 3 L TENSOR REMARK 3 L11: 2.3662 L22: 6.5231 REMARK 3 L33: 34.3643 L12: 2.2080 REMARK 3 L13: 6.0439 L23: 14.1609 REMARK 3 S TENSOR REMARK 3 S11: -0.1790 S12: 0.0954 S13: 0.1698 REMARK 3 S21: -0.4625 S22: -0.2149 S23: 0.2164 REMARK 3 S31: -1.4664 S32: -0.4698 S33: 0.3939 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 3 E 42 REMARK 3 ORIGIN FOR THE GROUP (A): -15.4450 2.4630 15.5460 REMARK 3 T TENSOR REMARK 3 T11: -0.2513 T22: -0.2660 REMARK 3 T33: -0.1101 T12: -0.0209 REMARK 3 T13: -0.0181 T23: 0.0361 REMARK 3 L TENSOR REMARK 3 L11: 1.3013 L22: 5.2940 REMARK 3 L33: 32.7305 L12: -0.3867 REMARK 3 L13: -2.5900 L23: 11.4717 REMARK 3 S TENSOR REMARK 3 S11: 0.1539 S12: -0.0529 S13: -0.0958 REMARK 3 S21: 0.2813 S22: -0.1906 S23: 0.0804 REMARK 3 S31: 0.3249 S32: -0.3893 S33: 0.0367 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 2 F 42 REMARK 3 ORIGIN FOR THE GROUP (A): -10.0020 11.1220 12.1430 REMARK 3 T TENSOR REMARK 3 T11: -0.2455 T22: -0.2139 REMARK 3 T33: -0.0456 T12: 0.0189 REMARK 3 T13: 0.0562 T23: 0.0451 REMARK 3 L TENSOR REMARK 3 L11: 1.5707 L22: 1.9545 REMARK 3 L33: 33.7861 L12: 0.8139 REMARK 3 L13: 0.9331 L23: 5.4030 REMARK 3 S TENSOR REMARK 3 S11: -0.0198 S12: 0.1484 S13: 0.1948 REMARK 3 S21: -0.1372 S22: 0.2057 S23: -0.1120 REMARK 3 S31: -0.6148 S32: 0.4642 S33: -0.1859 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3G9R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000051601. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAR-03 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22010 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 19.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.52800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1GCM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM HEPES, 0.1M AMMONIUM REMARK 280 DIHYDROGENPHOSPHATE, 50% MPD, PH 7.6, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298.0K 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 24.07850 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 6320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -96.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 REMARK 350 BIOMOLECULE: 2 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: 5840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F 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 GLU B 1 REMARK 465 LEU B 2 REMARK 465 GLU C 1 REMARK 465 LEU C 2 REMARK 465 GLU D 1 REMARK 465 GLU E 1 REMARK 465 LEU E 2 REMARK 465 GLU F 1 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),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 TRP C 19 CB TRP C 19 CG 0.110 REMARK 500 LYS D 4 CE LYS D 4 NZ 0.218 REMARK 500 LYS E 31 CE LYS E 31 NZ 0.189 REMARK 500 LYS E 42 CE LYS E 42 NZ 0.170 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 39 CG - CD - NE ANGL. DEV. = -14.2 DEGREES REMARK 500 ARG B 39 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG B 39 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ILE C 23 CG1 - CB - CG2 ANGL. DEV. = -13.4 DEGREES 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 LYS C 41 45.99 -94.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 43 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 44 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 45 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 46 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 47 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 48 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 43 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 44 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 C 43 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD C 44 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 D 43 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD E 43 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD E 44 DBREF 3G9R A 1 23 UNP Q4QX39 Q4QX39_9HIV1 655 677 DBREF 3G9R A 24 42 UNP P03069 GCN4_YEAST 258 276 DBREF 3G9R B 1 23 UNP Q4QX39 Q4QX39_9HIV1 655 677 DBREF 3G9R B 24 42 UNP P03069 GCN4_YEAST 258 276 DBREF 3G9R C 1 23 UNP Q4QX39 Q4QX39_9HIV1 655 677 DBREF 3G9R C 24 42 UNP P03069 GCN4_YEAST 258 276 DBREF 3G9R D 1 23 UNP Q4QX39 Q4QX39_9HIV1 655 677 DBREF 3G9R D 24 42 UNP P03069 GCN4_YEAST 258 276 DBREF 3G9R E 1 23 UNP Q4QX39 Q4QX39_9HIV1 655 677 DBREF 3G9R E 24 42 UNP P03069 GCN4_YEAST 258 276 DBREF 3G9R F 1 23 UNP Q4QX39 Q4QX39_9HIV1 655 677 DBREF 3G9R F 24 42 UNP P03069 GCN4_YEAST 258 276 SEQADV 3G9R LYS A 27 UNP P03069 LEU 261 ENGINEERED MUTATION SEQADV 3G9R ILE A 30 UNP P03069 ASN 264 ENGINEERED MUTATION SEQADV 3G9R LYS A 31 UNP P03069 TYR 265 ENGINEERED MUTATION SEQADV 3G9R ARG A 32 UNP P03069 HIS 266 ENGINEERED MUTATION SEQADV 3G9R ILE A 33 UNP P03069 LEU 267 ENGINEERED MUTATION SEQADV 3G9R ILE A 37 UNP P03069 VAL 271 ENGINEERED MUTATION SEQADV 3G9R LYS A 38 UNP P03069 ALA 272 ENGINEERED MUTATION SEQADV 3G9R ILE A 40 UNP P03069 LEU 274 ENGINEERED MUTATION SEQADV 3G9R LYS B 27 UNP P03069 LEU 261 ENGINEERED MUTATION SEQADV 3G9R ILE B 30 UNP P03069 ASN 264 ENGINEERED MUTATION SEQADV 3G9R LYS B 31 UNP P03069 TYR 265 ENGINEERED MUTATION SEQADV 3G9R ARG B 32 UNP P03069 HIS 266 ENGINEERED MUTATION SEQADV 3G9R ILE B 33 UNP P03069 LEU 267 ENGINEERED MUTATION SEQADV 3G9R ILE B 37 UNP P03069 VAL 271 ENGINEERED MUTATION SEQADV 3G9R LYS B 38 UNP P03069 ALA 272 ENGINEERED MUTATION SEQADV 3G9R ILE B 40 UNP P03069 LEU 274 ENGINEERED MUTATION SEQADV 3G9R LYS C 27 UNP P03069 LEU 261 ENGINEERED MUTATION SEQADV 3G9R ILE C 30 UNP P03069 ASN 264 ENGINEERED MUTATION SEQADV 3G9R LYS C 31 UNP P03069 TYR 265 ENGINEERED MUTATION SEQADV 3G9R ARG C 32 UNP P03069 HIS 266 ENGINEERED MUTATION SEQADV 3G9R ILE C 33 UNP P03069 LEU 267 ENGINEERED MUTATION SEQADV 3G9R ILE C 37 UNP P03069 VAL 271 ENGINEERED MUTATION SEQADV 3G9R LYS C 38 UNP P03069 ALA 272 ENGINEERED MUTATION SEQADV 3G9R ILE C 40 UNP P03069 LEU 274 ENGINEERED MUTATION SEQADV 3G9R LYS D 27 UNP P03069 LEU 261 ENGINEERED MUTATION SEQADV 3G9R ILE D 30 UNP P03069 ASN 264 ENGINEERED MUTATION SEQADV 3G9R LYS D 31 UNP P03069 TYR 265 ENGINEERED MUTATION SEQADV 3G9R ARG D 32 UNP P03069 HIS 266 ENGINEERED MUTATION SEQADV 3G9R ILE D 33 UNP P03069 LEU 267 ENGINEERED MUTATION SEQADV 3G9R ILE D 37 UNP P03069 VAL 271 ENGINEERED MUTATION SEQADV 3G9R LYS D 38 UNP P03069 ALA 272 ENGINEERED MUTATION SEQADV 3G9R ILE D 40 UNP P03069 LEU 274 ENGINEERED MUTATION SEQADV 3G9R LYS E 27 UNP P03069 LEU 261 ENGINEERED MUTATION SEQADV 3G9R ILE E 30 UNP P03069 ASN 264 ENGINEERED MUTATION SEQADV 3G9R LYS E 31 UNP P03069 TYR 265 ENGINEERED MUTATION SEQADV 3G9R ARG E 32 UNP P03069 HIS 266 ENGINEERED MUTATION SEQADV 3G9R ILE E 33 UNP P03069 LEU 267 ENGINEERED MUTATION SEQADV 3G9R ILE E 37 UNP P03069 VAL 271 ENGINEERED MUTATION SEQADV 3G9R LYS E 38 UNP P03069 ALA 272 ENGINEERED MUTATION SEQADV 3G9R ILE E 40 UNP P03069 LEU 274 ENGINEERED MUTATION SEQADV 3G9R LYS F 27 UNP P03069 LEU 261 ENGINEERED MUTATION SEQADV 3G9R ILE F 30 UNP P03069 ASN 264 ENGINEERED MUTATION SEQADV 3G9R LYS F 31 UNP P03069 TYR 265 ENGINEERED MUTATION SEQADV 3G9R ARG F 32 UNP P03069 HIS 266 ENGINEERED MUTATION SEQADV 3G9R ILE F 33 UNP P03069 LEU 267 ENGINEERED MUTATION SEQADV 3G9R ILE F 37 UNP P03069 VAL 271 ENGINEERED MUTATION SEQADV 3G9R LYS F 38 UNP P03069 ALA 272 ENGINEERED MUTATION SEQADV 3G9R ILE F 40 UNP P03069 LEU 274 ENGINEERED MUTATION SEQRES 1 A 42 GLU LEU ASP LYS TRP ALA SER LEU TRP ASN TRP PHE ASN SEQRES 2 A 42 ILE THR ASN TRP LEU TRP TYR ILE LYS ILE GLU GLU LEU SEQRES 3 A 42 LYS SER LYS ILE LYS ARG ILE GLU ASN GLU ILE LYS ARG SEQRES 4 A 42 ILE LYS LYS SEQRES 1 B 42 GLU LEU ASP LYS TRP ALA SER LEU TRP ASN TRP PHE ASN SEQRES 2 B 42 ILE THR ASN TRP LEU TRP TYR ILE LYS ILE GLU GLU LEU SEQRES 3 B 42 LYS SER LYS ILE LYS ARG ILE GLU ASN GLU ILE LYS ARG SEQRES 4 B 42 ILE LYS LYS SEQRES 1 C 42 GLU LEU ASP LYS TRP ALA SER LEU TRP ASN TRP PHE ASN SEQRES 2 C 42 ILE THR ASN TRP LEU TRP TYR ILE LYS ILE GLU GLU LEU SEQRES 3 C 42 LYS SER LYS ILE LYS ARG ILE GLU ASN GLU ILE LYS ARG SEQRES 4 C 42 ILE LYS LYS SEQRES 1 D 42 GLU LEU ASP LYS TRP ALA SER LEU TRP ASN TRP PHE ASN SEQRES 2 D 42 ILE THR ASN TRP LEU TRP TYR ILE LYS ILE GLU GLU LEU SEQRES 3 D 42 LYS SER LYS ILE LYS ARG ILE GLU ASN GLU ILE LYS ARG SEQRES 4 D 42 ILE LYS LYS SEQRES 1 E 42 GLU LEU ASP LYS TRP ALA SER LEU TRP ASN TRP PHE ASN SEQRES 2 E 42 ILE THR ASN TRP LEU TRP TYR ILE LYS ILE GLU GLU LEU SEQRES 3 E 42 LYS SER LYS ILE LYS ARG ILE GLU ASN GLU ILE LYS ARG SEQRES 4 E 42 ILE LYS LYS SEQRES 1 F 42 GLU LEU ASP LYS TRP ALA SER LEU TRP ASN TRP PHE ASN SEQRES 2 F 42 ILE THR ASN TRP LEU TRP TYR ILE LYS ILE GLU GLU LEU SEQRES 3 F 42 LYS SER LYS ILE LYS ARG ILE GLU ASN GLU ILE LYS ARG SEQRES 4 F 42 ILE LYS LYS HET PO4 A 43 5 HET PO4 A 44 5 HET MPD A 45 8 HET MPD A 46 8 HET MPD A 47 8 HET MPD A 48 8 HET PO4 B 43 5 HET MPD B 44 8 HET PO4 C 43 5 HET MPD C 44 8 HET PO4 D 43 5 HET MPD E 43 8 HET MPD E 44 8 HETNAM PO4 PHOSPHATE ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 7 PO4 5(O4 P 3-) FORMUL 9 MPD 8(C6 H14 O2) FORMUL 20 HOH *78(H2 O) HELIX 1 1 GLU A 1 LYS A 42 1 42 HELIX 2 2 ASP B 3 LYS B 42 1 40 HELIX 3 3 ASP C 3 LYS C 41 1 39 HELIX 4 4 ASP D 3 LYS D 42 1 40 HELIX 5 5 ASP E 3 LYS E 42 1 40 HELIX 6 6 ASP F 3 LYS F 42 1 40 SITE 1 AC1 1 ARG A 32 SITE 1 AC2 2 ARG A 39 LYS A 42 SITE 1 AC3 1 ASN A 10 SITE 1 AC4 8 PHE A 12 THR A 15 ASN A 16 ASN B 16 SITE 2 AC4 8 PHE C 12 THR C 15 ASN C 16 TRP C 19 SITE 1 AC5 3 LYS A 27 LYS A 31 LYS E 27 SITE 1 AC6 1 GLU A 1 SITE 1 AC7 1 ARG B 39 SITE 1 AC8 4 LYS A 22 LYS B 27 LYS E 22 LYS F 27 SITE 1 AC9 2 ARG C 39 LYS C 42 SITE 1 BC1 1 TRP D 11 SITE 1 BC2 3 TRP A 9 SER C 7 TRP C 11 SITE 1 BC3 11 PHE D 12 THR D 15 ASN D 16 TRP D 19 SITE 2 BC3 11 PHE E 12 ASN E 16 TRP E 19 TRP F 11 SITE 3 BC3 11 THR F 15 ASN F 16 TRP F 19 SITE 1 BC4 3 TRP C 17 TRP D 11 ASN E 13 CRYST1 42.527 48.157 81.782 90.00 95.38 90.00 P 1 21 1 12 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 0.023514 0.000000 0.002214 0.00000 SCALE2 0.000000 0.020765 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012282 0.00000