HEADER HYDROLASE 11-MAR-15 4YOB TITLE CRYSTAL STRUCTURE OF APO HIV-1 PROTEASE MDR769 L33F COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 PROTEASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 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-1 PROTEASE, MDR769 33F, MOLECULAR ANCHOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.D.KUIPER,B.KEUSCH,T.G.DEWDNEY,P.CHORDIA,K.ROSS,J.S.BRUNZELLE, AUTHOR 2 I.A.KOVARI,R.MACARTHUR,H.SALIMNIA,L.C.KOVARI REVDAT 4 28-FEB-24 4YOB 1 REMARK REVDAT 3 30-MAR-22 4YOB 1 REMARK REVDAT 2 18-APR-18 4YOB 1 SOURCE JRNL REMARK REVDAT 1 08-JUL-15 4YOB 0 JRNL AUTH B.D.KUIPER,B.J.KEUSCH,T.G.DEWDNEY,P.CHORDIA,K.ROSS, JRNL AUTH 2 J.S.BRUNZELLE,I.A.KOVARI,R.MACARTHUR,H.SALIMNIA,L.C.KOVARI JRNL TITL THE L33F DARUNAVIR RESISTANCE MUTATION ACTS AS A MOLECULAR JRNL TITL 2 ANCHOR REDUCING THE FLEXIBILITY OF THE HIV-1 PROTEASE 30S JRNL TITL 3 AND 80S LOOPS. JRNL REF BIOCHEM BIOPHYS REP V. 2 160 2015 JRNL REFN ESSN 2405-5808 JRNL PMID 29124158 JRNL DOI 10.1016/J.BBREP.2015.06.003 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 17773 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 907 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 27.3324 - 2.7321 1.00 3039 154 0.1632 0.1632 REMARK 3 2 2.7321 - 2.1688 0.99 2844 148 0.1823 0.1921 REMARK 3 3 2.1688 - 1.8947 0.99 2805 145 0.1756 0.2256 REMARK 3 4 1.8947 - 1.7215 0.98 2751 161 0.1858 0.2461 REMARK 3 5 1.7215 - 1.5981 0.98 2719 150 0.2023 0.2155 REMARK 3 6 1.5981 - 1.5040 0.98 2708 149 0.2372 0.2957 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.920 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 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 : 0.007 800 REMARK 3 ANGLE : 0.984 1093 REMARK 3 CHIRALITY : 0.043 130 REMARK 3 PLANARITY : 0.005 140 REMARK 3 DIHEDRAL : 13.574 300 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 1:99) REMARK 3 ORIGIN FOR THE GROUP (A): -2.5839 4.0595 -14.0803 REMARK 3 T TENSOR REMARK 3 T11: 0.1088 T22: 0.1228 REMARK 3 T33: 0.1218 T12: -0.0230 REMARK 3 T13: 0.0102 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 0.9308 L22: 0.7871 REMARK 3 L33: 1.6363 L12: -0.2805 REMARK 3 L13: -0.1569 L23: 0.5966 REMARK 3 S TENSOR REMARK 3 S11: 0.0072 S12: -0.0386 S13: 0.0441 REMARK 3 S21: 0.0574 S22: -0.0425 S23: 0.0378 REMARK 3 S31: 0.0965 S32: -0.0737 S33: -0.0011 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 4YOB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207817. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : KOHZU REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17812 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 102.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 14.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4M AMMONIUM SULFATE, 0.1 M MES, PH REMARK 280 6.2; 2.4 M AMMONIUM SULFATE, 0.1 M HEPES, PH 6.8, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.11000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.87700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.87700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.55500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.87700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.87700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.66500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.87700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.87700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.55500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.87700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.87700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 76.66500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.11000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -51.11000 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 162 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 178 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 O HOH A 211 O HOH A 219 1.90 REMARK 500 O HOH A 146 O HOH A 166 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 152 O HOH A 152 7555 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 223 DISTANCE = 5.95 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YOA RELATED DB: PDB DBREF 4YOB A 1 99 UNP Q5RTL1 Q5RTL1_9HIV1 1 99 SEQADV 4YOB LYS A 7 UNP Q5RTL1 GLN 7 ENGINEERED MUTATION SEQADV 4YOB ASN A 25 UNP Q5RTL1 ASP 25 ENGINEERED MUTATION SEQADV 4YOB PHE A 33 UNP Q5RTL1 LEU 33 ENGINEERED MUTATION SEQADV 4YOB VAL A 36 UNP Q5RTL1 MET 36 ENGINEERED MUTATION SEQADV 4YOB THR A 82 UNP Q5RTL1 ALA 82 ENGINEERED MUTATION SEQADV 4YOB VAL A 84 UNP Q5RTL1 ILE 84 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN ILE THR LEU TRP LYS ARG PRO ILE VAL THR ILE SEQRES 2 A 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASN THR SEQRES 3 A 99 GLY ALA ASP ASP THR VAL PHE GLU GLU VAL ASN LEU PRO SEQRES 4 A 99 GLY ARG TRP LYS PRO LYS LEU ILE GLY GLY ILE GLY GLY SEQRES 5 A 99 PHE VAL LYS VAL ARG GLN TYR ASP GLN VAL PRO ILE GLU SEQRES 6 A 99 ILE CYS GLY HIS LYS VAL ILE GLY THR VAL LEU VAL GLY SEQRES 7 A 99 PRO THR PRO THR ASN VAL ILE GLY ARG ASN LEU MET THR SEQRES 8 A 99 GLN ILE GLY CYS THR LEU ASN PHE FORMUL 2 HOH *134(H2 O) HELIX 1 AA1 GLY A 86 THR A 91 1 6 SHEET 1 AA1 8 LYS A 43 GLY A 48 0 SHEET 2 AA1 8 PHE A 53 ILE A 66 -1 O GLN A 58 N LYS A 43 SHEET 3 AA1 8 HIS A 69 VAL A 77 -1 O VAL A 71 N ILE A 64 SHEET 4 AA1 8 VAL A 32 PHE A 33 1 N PHE A 33 O LEU A 76 SHEET 5 AA1 8 VAL A 84 ILE A 85 -1 O VAL A 84 N VAL A 32 SHEET 6 AA1 8 GLN A 18 LEU A 24 1 N LEU A 23 O ILE A 85 SHEET 7 AA1 8 ILE A 10 ILE A 15 -1 N ILE A 13 O LYS A 20 SHEET 8 AA1 8 PHE A 53 ILE A 66 -1 O GLU A 65 N LYS A 14 CRYST1 45.754 45.754 102.220 90.00 90.00 90.00 P 41 21 2 8 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 0.021856 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021856 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009783 0.00000