HEADER VIRAL PROTEIN 21-DEC-20 7DPQ TITLE HIV-1 PROTEASE D30N MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RETROPEPSIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: POL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HIV PROTEASE, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.C.BIHANI,M.V.HOSUR REVDAT 2 29-NOV-23 7DPQ 1 REMARK REVDAT 1 03-NOV-21 7DPQ 0 JRNL AUTH S.C.BIHANI,G.D.GUPTA,M.V.HOSUR JRNL TITL MOLECULAR BASIS FOR REDUCED CLEAVAGE ACTIVITY AND DRUG JRNL TITL 2 RESISTANCE IN D30N HIV-1 PROTEASE. JRNL REF J.BIOMOL.STRUCT.DYN. 1 2021 JRNL REFN ESSN 1538-0254 JRNL PMID 34609269 JRNL DOI 10.1080/07391102.2021.1982007 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 21748 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1088 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 45.1600 - 3.3000 0.98 2584 137 0.1752 0.1959 REMARK 3 2 3.3000 - 2.6200 1.00 2605 137 0.1936 0.2278 REMARK 3 3 2.6200 - 2.2900 1.00 2587 136 0.1958 0.2394 REMARK 3 4 2.2900 - 2.0800 1.00 2587 136 0.1914 0.2061 REMARK 3 5 2.0800 - 1.9300 1.00 2592 137 0.1908 0.2599 REMARK 3 6 1.9300 - 1.8200 1.00 2594 136 0.2073 0.2458 REMARK 3 7 1.8200 - 1.7300 1.00 2566 135 0.2270 0.3086 REMARK 3 8 1.7300 - 1.6500 0.99 2545 134 0.2394 0.2883 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) : 0.204 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.274 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.75 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 : 0.006 1542 REMARK 3 ANGLE : 0.878 2089 REMARK 3 CHIRALITY : 0.061 250 REMARK 3 PLANARITY : 0.005 261 REMARK 3 DIHEDRAL : 16.909 582 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 99 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.2313 16.7926 19.1195 REMARK 3 T TENSOR REMARK 3 T11: 0.1189 T22: 0.1490 REMARK 3 T33: 0.1276 T12: -0.0099 REMARK 3 T13: -0.0033 T23: -0.0240 REMARK 3 L TENSOR REMARK 3 L11: 2.7400 L22: 1.0193 REMARK 3 L33: 2.2431 L12: 0.5242 REMARK 3 L13: 1.3734 L23: 0.4150 REMARK 3 S TENSOR REMARK 3 S11: 0.0328 S12: 0.3147 S13: -0.1996 REMARK 3 S21: -0.0780 S22: 0.0486 S23: 0.0167 REMARK 3 S31: 0.1062 S32: 0.1587 S33: -0.0229 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1001 THROUGH 1099 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.9672 23.3212 36.4767 REMARK 3 T TENSOR REMARK 3 T11: 0.1396 T22: 0.1293 REMARK 3 T33: 0.1366 T12: -0.0094 REMARK 3 T13: -0.0224 T23: 0.0114 REMARK 3 L TENSOR REMARK 3 L11: 1.8944 L22: 2.0932 REMARK 3 L33: 1.8959 L12: 1.2547 REMARK 3 L13: 0.7816 L23: 1.2124 REMARK 3 S TENSOR REMARK 3 S11: 0.1170 S12: -0.0917 S13: -0.0934 REMARK 3 S21: 0.2802 S22: -0.0334 S23: -0.2249 REMARK 3 S31: 0.2074 S32: 0.0370 S33: -0.0401 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 7DPQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1300019903. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21751 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 45.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.58100 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: PHENIX REMARK 200 STARTING MODEL: 3KT2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1-5% SATURATED AMMONIUM SULFATE, 200 REMARK 280 MM /100 MM PHOSPHATE CITRATE BUFFER PH 6.2, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 27.43333 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 54.86667 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 41.15000 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 68.58333 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 13.71667 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 DBREF 7DPQ A 1 99 UNP Q72874 Q72874_9HIV1 1 99 DBREF 7DPQ A 1001 1099 UNP Q72874 Q72874_9HIV1 1 99 SEQADV 7DPQ ASN A 30 UNP Q72874 ASP 30 ENGINEERED MUTATION SEQADV 7DPQ MET A 95 UNP Q72874 CYS 95 ENGINEERED MUTATION SEQADV 7DPQ GLY A 996 UNP Q72874 LINKER SEQADV 7DPQ GLY A 997 UNP Q72874 LINKER SEQADV 7DPQ SER A 998 UNP Q72874 LINKER SEQADV 7DPQ SER A 999 UNP Q72874 LINKER SEQADV 7DPQ GLY A 1000 UNP Q72874 LINKER SEQADV 7DPQ ASN A 1030 UNP Q72874 ASP 30 ENGINEERED MUTATION SEQADV 7DPQ ALA A 1095 UNP Q72874 CYS 95 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 ASN 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 CSO 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 ASN 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 CSO 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 MODRES 7DPQ CSO A 67 CYS MODIFIED RESIDUE MODRES 7DPQ CSO A 1067 CYS MODIFIED RESIDUE HET CSO A 67 7 HET CSO A1067 7 HETNAM CSO S-HYDROXYCYSTEINE FORMUL 1 CSO 2(C3 H7 N O3 S) FORMUL 2 HOH *178(H2 O) HELIX 1 AA1 GLY A 86 THR A 91 1 6 HELIX 2 AA2 GLN A 92 GLY A 94 5 3 HELIX 3 AA3 GLY A 1086 THR A 1091 1 6 HELIX 4 AA4 GLN A 1092 GLY A 1094 5 3 SHEET 1 AA1 3 GLN A 2 VAL A 3 0 SHEET 2 AA1 3 THR A1096 ASN A1098 -1 O LEU A1097 N VAL A 3 SHEET 3 AA1 3 THR A 96 ASN A 98 -1 N ASN A 98 O THR A1096 SHEET 1 AA2 8 LYS A 43 GLY A 49 0 SHEET 2 AA2 8 GLY A 52 ILE A 66 -1 O GLN A 58 N LYS A 43 SHEET 3 AA2 8 HIS A 69 VAL A 77 -1 O HIS A 69 N ILE A 66 SHEET 4 AA2 8 VAL A 32 LEU A 33 1 N LEU A 33 O LEU A 76 SHEET 5 AA2 8 ILE A 84 ILE A 85 -1 O ILE A 84 N VAL A 32 SHEET 6 AA2 8 GLN A 18 LEU A 24 1 N LEU A 23 O ILE A 85 SHEET 7 AA2 8 LEU A 10 ILE A 15 -1 N ILE A 13 O LYS A 20 SHEET 8 AA2 8 GLY A 52 ILE A 66 -1 O GLU A 65 N LYS A 14 SHEET 1 AA3 8 LYS A1043 GLY A1049 0 SHEET 2 AA3 8 GLY A1052 ILE A1066 -1 O VAL A1056 N LYS A1045 SHEET 3 AA3 8 HIS A1069 VAL A1077 -1 O HIS A1069 N ILE A1066 SHEET 4 AA3 8 VAL A1032 LEU A1033 1 N LEU A1033 O LEU A1076 SHEET 5 AA3 8 ILE A1084 ILE A1085 -1 O ILE A1084 N VAL A1032 SHEET 6 AA3 8 GLN A1018 LEU A1024 1 N LEU A1023 O ILE A1085 SHEET 7 AA3 8 LEU A1010 ILE A1015 -1 N ILE A1013 O LYS A1020 SHEET 8 AA3 8 GLY A1052 ILE A1066 -1 O GLU A1065 N LYS A1014 LINK C ILE A 66 N CSO A 67 1555 1555 1.33 LINK C CSO A 67 N GLY A 68 1555 1555 1.33 LINK C ILE A1066 N CSO A1067 1555 1555 1.33 LINK C CSO A1067 N GLY A1068 1555 1555 1.33 CRYST1 62.370 62.370 82.300 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 0.016033 0.009257 0.000000 0.00000 SCALE2 0.000000 0.018514 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012151 0.00000