PDB Short entry for 1LV1 HEADER HYDROLASE 24-MAY-02 1LV1 TITLE CRYSTAL STRUCTURE ANALYSIS OF THE NON-ACTIVE SITE MUTANT OF TETHERED TITLE 2 HIV-1 PROTEASE TO 2.1A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 PROTEASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.23.16; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: TETHERED DIMER LINKED BY GGSSG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS BETA-RIBBON FLAP, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KUMAR,K.K.KANNAN,M.V.HOSUR,N.S.BHAVESH,A.CHATTERJEE,R.MITTAL, AUTHOR 2 R.V.HOSUR REVDAT 5 10-NOV-21 1LV1 1 SEQADV REVDAT 4 16-AUG-17 1LV1 1 SOURCE REMARK REVDAT 3 24-FEB-09 1LV1 1 VERSN REVDAT 2 20-NOV-02 1LV1 1 REMARK REVDAT 1 19-JUN-02 1LV1 0 JRNL AUTH M.KUMAR,K.K.KANNAN,M.V.HOSUR,N.S.BHAVESH,A.CHATTERJEE, JRNL AUTH 2 R.MITTAL,R.V.HOSUR JRNL TITL EFFECTS OF REMOTE MUTATION ON THE AUTOLYSIS OF HIV-1 PR: JRNL TITL 2 X-RAY AND NMR INVESTIGATIONS. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 294 395 2002 JRNL REFN ISSN 0006-291X JRNL PMID 12051725 JRNL DOI 10.1016/S0006-291X(02)00482-5 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 319647.950 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 73.3 REMARK 3 NUMBER OF REFLECTIONS : 8047 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) : 0.194 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 428 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 47.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 610 REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE : 0.3920 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 30 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.072 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1513 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 55 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.95000 REMARK 3 B22 (A**2) : 0.95000 REMARK 3 B33 (A**2) : -1.91000 REMARK 3 B12 (A**2) : 6.10000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.27 REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.36 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.490 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.430 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.300 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.380 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 53.99 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1LV1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-MAY-02. REMARK 100 THE DEPOSITION ID IS D_1000016300. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-01 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 6.2 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 RU200HB REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : TOTALLY REFLECTING MSC 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 : 11676 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 47.0 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 <I/SIGMA(I)> 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: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% SATURATED AMMONIUM SULFATE, 200MM REMARK 280 SODIUM PHOSPHATE, PH 6.2, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 27.80667 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 55.61333 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 41.71000 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 69.51667 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 13.90333 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: MONOMERIC 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 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 GLY A 996 REMARK 465 GLY A 997 REMARK 465 SER A 998 REMARK 465 SER A 999 REMARK 465 GLY A 1000 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 CYS A1067 43.63 33.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G6L RELATED DB: PDB REMARK 900 1G6L CONTAINS THE TETHERED HIV-1 PROTEASE CARRYING THE SINGLE REMARK 900 MUTATION C95M ON ONE SUBUNIT ONLY. DBREF 1LV1 A 1 99 UNP P04585 POL_HV1H2 57 155 DBREF 1LV1 A 1001 1099 UNP P04585 POL_HV1H2 57 155 SEQADV 1LV1 MET A 95 UNP P04585 CYS 151 ENGINEERED MUTATION SEQADV 1LV1 GLY A 996 UNP P04585 LINKER SEQADV 1LV1 GLY A 997 UNP P04585 LINKER SEQADV 1LV1 SER A 998 UNP P04585 LINKER SEQADV 1LV1 SER A 999 UNP P04585 LINKER SEQADV 1LV1 GLY A 1000 UNP P04585 LINKER SEQADV 1LV1 ALA A 1095 UNP P04585 CYS 151 ENGINEERED MUTATION SEQRES 1 A 203 PRO GLN VAL THR LEU TRP GLN ARG PRO LEU VAL THR ILE SEQRES 2 A 203 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 A 203 GLY ALA ASP ASP THR VAL LEU GLU GLU MET SER LEU PRO SEQRES 4 A 203 GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 A 203 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE LEU ILE GLU SEQRES 6 A 203 ILE CYS GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 A 203 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 A 203 GLN ILE GLY MET THR LEU ASN PHE GLY GLY SER SER GLY SEQRES 9 A 203 PRO GLN VAL THR LEU TRP GLN ARG PRO LEU VAL THR ILE SEQRES 10 A 203 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 11 A 203 GLY ALA ASP ASP THR VAL LEU GLU GLU MET SER LEU PRO SEQRES 12 A 203 GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 13 A 203 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE LEU ILE GLU SEQRES 14 A 203 ILE CYS GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 15 A 203 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 16 A 203 GLN ILE GLY ALA THR LEU ASN PHE FORMUL 2 HOH *55(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLN A 92 GLY A 94 5 3 HELIX 3 3 GLY A 1086 THR A 1091 1 6 HELIX 4 4 GLN A 1092 GLY A 1094 5 3 SHEET 1 A 4 GLN A 2 VAL A 3 0 SHEET 2 A 4 THR A1096 ASN A1098 -1 O LEU A1097 N VAL A 3 SHEET 3 A 4 THR A 96 ASN A 98 -1 N THR A 96 O ASN A1098 SHEET 4 A 4 GLN A1002 THR A1004 -1 N VAL A1003 O LEU A 97 SHEET 1 B 8 LYS A 43 GLY A 49 0 SHEET 2 B 8 GLY A 52 ILE A 66 -1 O GLY A 52 N GLY A 49 SHEET 3 B 8 LEU A 10 ILE A 15 -1 O LYS A 14 N GLU A 65 SHEET 4 B 8 GLN A 18 LEU A 24 -1 O GLN A 18 N ILE A 15 SHEET 5 B 8 ILE A 84 ILE A 85 1 N ILE A 85 O LEU A 23 SHEET 6 B 8 VAL A 32 LEU A 33 -1 O VAL A 32 N ILE A 84 SHEET 7 B 8 HIS A 69 VAL A 77 1 O LEU A 76 N LEU A 33 SHEET 8 B 8 GLY A 52 ILE A 66 -1 N ARG A 57 O VAL A 77 SHEET 1 C 8 LYS A1043 GLY A1049 0 SHEET 2 C 8 GLY A1052 ILE A1066 -1 O GLY A1052 N GLY A1049 SHEET 3 C 8 LEU A1010 ILE A1015 -1 O LYS A1014 N GLU A1065 SHEET 4 C 8 GLN A1018 LEU A1024 -1 O GLN A1018 N ILE A1015 SHEET 5 C 8 ILE A1084 ILE A1085 1 N ILE A1085 O LEU A1023 SHEET 6 C 8 VAL A1032 LEU A1033 -1 O VAL A1032 N ILE A1084 SHEET 7 C 8 HIS A1069 VAL A1077 1 O LEU A1076 N LEU A1033 SHEET 8 C 8 GLY A1052 ILE A1066 -1 N ARG A1057 O VAL A1077 CRYST1 63.060 63.060 83.420 90.00 90.00 120.00 P 61 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 0.015858 0.009156 0.000000 0.00000 SCALE2 0.000000 0.018311 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011988 0.00000