PDB Short entry for 1AIK HEADER VIRAL PROTEIN 20-APR-97 1AIK TITLE HIV GP41 CORE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 GP41 GLYCOPROTEIN; COMPND 3 CHAIN: N; COMPND 4 FRAGMENT: PROTEASE-RESISTANT CORE; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: N36 AND C34 ARE SYNTHETIC PEPTIDES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HIV-1 GP41 GLYCOPROTEIN; COMPND 9 CHAIN: C; COMPND 10 FRAGMENT: PROTEASE-RESISTANT CORE; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: N36 AND C34 ARE SYNTHETIC PEPTIDES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HIV-1 M:B_HXB2R; SOURCE 3 ORGANISM_TAXID: 11706; SOURCE 4 STRAIN: HXB2; SOURCE 5 CELLULAR_LOCATION: VIRAL MEMBRANE; SOURCE 6 GENE: GP41; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_GENE: GP41; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HIV-1 M:B_HXB2R; SOURCE 12 ORGANISM_TAXID: 11706; SOURCE 13 STRAIN: HXB2; SOURCE 14 CELLULAR_LOCATION: VIRAL MEMBRANE; SOURCE 15 GENE: GP41; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_GENE: GP41 KEYWDS HIV, GP41, ENVELOPE GLYCOPROTEIN, RETROVIRUS, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.C.CHAN,D.FASS,J.M.BERGER,P.S.KIM REVDAT 3 13-JUL-11 1AIK 1 VERSN REVDAT 2 24-FEB-09 1AIK 1 VERSN REVDAT 1 16-JUN-97 1AIK 0 JRNL AUTH D.C.CHAN,D.FASS,J.M.BERGER,P.S.KIM JRNL TITL CORE STRUCTURE OF GP41 FROM THE HIV ENVELOPE GLYCOPROTEIN. JRNL REF CELL(CAMBRIDGE,MASS.) V. 89 263 1997 JRNL REFN ISSN 0092-8674 JRNL PMID 9108481 JRNL DOI 10.1016/S0092-8674(00)80205-6 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 5683 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) : 0.238 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.120 REMARK 3 FREE R VALUE TEST SET COUNT : 371 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 : 594 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 43 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) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 2.74 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 1AIK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : MAR-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5287 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.4000 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: X-PLOR 3.851 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: DATA AT NSLS USED MAD METHODS. DATA COLLECTED ON AN OSMIUM REMARK 200 -SOAK CRYSTAL AT WAVELENGTHS 1.1398, 1.1396, 1.1344, AND 1.1406 REMARK 200 ANGSTROMS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: A 10 MG/ML STOCK WAS DILUTED 1:1 IN A REMARK 280 SITTING DROP WITH 80 MM NH4CL, 20% PEG200, AND 50% ISOPROPANOL, REMARK 280 AND THEN ALLOWED TO EQUILIBRATE AGAINST 80 MM NH4CL, 20% PEG200, REMARK 280 AND 30% ISOPROPANOL., PH 6.0, VAPOR DIFFUSION - SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 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 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 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 12190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -98.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: N, 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 BIOMT1 2 -0.500000 -0.866025 0.000000 49.50000 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 24.75000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 42.86826 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 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 H GLU C 630 H1 HOH C 8 1.41 REMARK 500 H SER N 546 H1 HOH N 29 1.50 REMARK 500 REMARK 500 REMARK: NULL 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 HIS N 564 NE2 HIS N 564 CD2 -0.082 REMARK 500 HIS C 643 NE2 HIS C 643 CD2 -0.085 REMARK 500 SER C 644 CB SER C 644 OG 0.083 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 TRP N 571 CD1 - CG - CD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 TRP N 571 CE2 - CD2 - CG ANGL. DEV. = -5.8 DEGREES REMARK 500 TRP N 571 CG - CD2 - CE3 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG N 579 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 TRP C 628 CD1 - CG - CD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 TRP C 628 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 TRP C 631 CD1 - CG - CD2 ANGL. DEV. = 7.4 DEGREES REMARK 500 TRP C 631 CG - CD1 - NE1 ANGL. DEV. = -6.1 DEGREES REMARK 500 TRP C 631 CE2 - CD2 - CG ANGL. DEV. = -5.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1AIK N 546 581 UNP P04578 ENV_HV1H2 544 579 DBREF 1AIK C 628 661 UNP P04578 ENV_HV1H2 623 656 SEQRES 1 N 37 ACE SER GLY ILE VAL GLN GLN GLN ASN ASN LEU LEU ARG SEQRES 2 N 37 ALA ILE GLU ALA GLN GLN HIS LEU LEU GLN LEU THR VAL SEQRES 3 N 37 TRP GLY ILE LYS GLN LEU GLN ALA ARG ILE LEU SEQRES 1 C 35 ACE TRP MET GLU TRP ASP ARG GLU ILE ASN ASN TYR THR SEQRES 2 C 35 SER LEU ILE HIS SER LEU ILE GLU GLU SER GLN ASN GLN SEQRES 3 C 35 GLN GLU LYS ASN GLU GLN GLU LEU LEU HET ACE N 545 3 HET ACE C 627 3 HETNAM ACE ACETYL GROUP FORMUL 1 ACE 2(C2 H4 O) FORMUL 3 HOH *43(H2 O) HELIX 1 1 GLY N 547 ALA N 578 1 32 HELIX 2 2 MET C 629 GLU C 659 1 31 LINK C ACE N 545 N SER N 546 1555 1555 1.33 LINK C ACE C 627 N TRP C 628 1555 1555 1.33 CRYST1 49.500 49.500 55.300 90.00 90.00 120.00 P 3 2 1 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 0.020202 0.011664 0.000000 0.00000 SCALE2 0.000000 0.023327 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018083 0.00000 HETATM 1 C ACE N 545 19.211 14.270 -17.472 1.00 56.26 C HETATM 2 O ACE N 545 19.488 14.580 -16.305 1.00 56.37 O HETATM 3 CH3 ACE N 545 20.273 14.045 -18.531 1.00 56.01 C