HEADER HYDROLASE 19-JUN-19 6S1V TITLE CRYSTAL STRUCTURE OF DIMERIC M-PMV PROTEASE D26N MUTANT IN COMPLEX TITLE 2 WITH INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG-PRO-POL POLYPROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PR180; COMPND 5 EC: 3.6.1.23,3.4.23.-,2.7.7.49,2.7.7.7,3.1.26.4,2.7.7.-,3.1.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: GAPS IN THE SEQUENCE INDICATE RESIDUES THAT WERE NOT COMPND 9 MODELED BECAUSE OF POOR ELECTRON DENSITY; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: PRO-0A1-VAL-PSA-ALA-MET-THR; COMPND 12 CHAIN: I; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: IN THE STANDARD DEFINITION USED BY REFMAC, THE CGAMMA COMPND 15 ATOM OF THE PSA RESIDUE IS LABELED AS CA. IN THE PDB VALIDATION COMPND 16 REPORT THIS LABEL IS INTERPRETED AS CALPHA CAUSING GEOMETRICAL COMPND 17 ALERTS. THESE ALERTS ARE FALSE AND SHOULD BE IGNORED. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MASON-PFIZER MONKEY VIRUS; SOURCE 3 ORGANISM_COMMON: MPMV; SOURCE 4 ORGANISM_TAXID: 11855; SOURCE 5 GENE: GAG-PRO-POL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PBPS13ATG; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS MASON-PFIZER MONKEY VIRUS, M-PMV, RETROVIRUS, RETROPEPSIN, ASPARTIC KEYWDS 2 PROTEASE, DIMERIZATION, INHIBITOR, FLAP STRUCTURE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.WOSICKI,M.GILSKI,M.JASKOLSKI,H.ZABRANSKA,I.PICHOVA REVDAT 2 24-JAN-24 6S1V 1 LINK REVDAT 1 16-OCT-19 6S1V 0 JRNL AUTH S.WOSICKI,M.GILSKI,H.ZABRANSKA,I.PICHOVA,M.JASKOLSKI JRNL TITL COMPARISON OF A RETROVIRAL PROTEASE IN MONOMERIC AND DIMERIC JRNL TITL 2 STATES. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 75 904 2019 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 31588922 JRNL DOI 10.1107/S2059798319011355 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.KHATIB,F.DIMAIO,S.COOPER,M.KAZMIERCZYK,M.GILSKI,S.KRZYWDA, REMARK 1 AUTH 2 H.ZABRANSKA,I.PICHOVA,J.THOMPSON,Z.POPOVIC,M.JASKOLSKI, REMARK 1 AUTH 3 D.BAKER REMARK 1 TITL CRYSTAL STRUCTURE OF A MONOMERIC RETROVIRAL PROTEASE SOLVED REMARK 1 TITL 2 BY PROTEIN FOLDING GAME PLAYERS. REMARK 1 REF NAT.STRUCT.MOL.BIOL. V. 18 1175 2011 REMARK 1 REFN ESSN 1545-9985 REMARK 1 PMID 21926992 REMARK 1 DOI 10.1038/NSMB.2119 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.GILSKI,M.KAZMIERCZYK,S.KRZYWDA,H.ZABRANSKA,S.COOPER, REMARK 1 AUTH 2 Z.POPOVIC,F.KHATIB,F.DIMAIO,J.THOMPSON,D.BAKER,I.PICHOVA, REMARK 1 AUTH 3 M.JASKOLSKI REMARK 1 TITL HIGH-RESOLUTION STRUCTURE OF A RETROVIRAL PROTEASE FOLDED AS REMARK 1 TITL 2 A MONOMER. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 67 907 2011 REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 22101816 REMARK 1 DOI 10.1107/S0907444911035943 REMARK 1 REFERENCE 3 REMARK 1 AUTH M.MILLER,M.JASKOLSKI,J.K.RAO,J.LEIS,A.WLODAWER REMARK 1 TITL CRYSTAL STRUCTURE OF A RETROVIRAL PROTEASE PROVES REMARK 1 TITL 2 RELATIONSHIP TO ASPARTIC PROTEASE FAMILY. REMARK 1 REF NATURE V. 337 576 1989 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 2536902 REMARK 1 DOI 10.1038/337576A0 REMARK 1 REFERENCE 4 REMARK 1 AUTH A.WLODAWER,M.MILLER,M.JASKOLSKI,B.K.SATHYANARAYANA, REMARK 1 AUTH 2 E.BALDWIN,I.T.WEBER,L.M.SELK,L.CLAWSON,J.SCHNEIDER,S.B.KENT REMARK 1 TITL CONSERVED FOLDING IN RETROVIRAL PROTEASES: CRYSTAL STRUCTURE REMARK 1 TITL 2 OF A SYNTHETIC HIV-1 PROTEASE. REMARK 1 REF SCIENCE V. 245 616 1989 REMARK 1 REFN ISSN 0036-8075 REMARK 1 PMID 2548279 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0232 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 29403 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1004 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) : 1.64 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.68 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2075 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.3580 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.3670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1733 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 157 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.35000 REMARK 3 B22 (A**2) : -0.76000 REMARK 3 B33 (A**2) : -0.22000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.82000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.089 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.094 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.119 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1823 ; 0.015 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1696 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2496 ; 1.701 ; 1.640 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3975 ; 1.360 ; 1.574 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 218 ; 8.619 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 74 ;36.882 ;25.405 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 317 ;15.046 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ; 8.397 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 249 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1949 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 329 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 876 ; 2.754 ; 2.889 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 875 ; 2.749 ; 2.881 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1089 ; 4.144 ; 4.270 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1090 ; 4.142 ; 4.280 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 947 ; 3.463 ; 3.292 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 947 ; 3.454 ; 3.292 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1405 ; 5.247 ; 4.807 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2065 ; 8.846 ;34.702 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2035 ; 8.831 ;34.274 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 108 B 1 108 3031 0.13 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 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 7 REMARK 3 ORIGIN FOR THE GROUP (A): 23.5791 -4.9519 22.1589 REMARK 3 T TENSOR REMARK 3 T11: 0.3002 T22: 0.1251 REMARK 3 T33: 0.0435 T12: 0.1000 REMARK 3 T13: -0.0246 T23: 0.0304 REMARK 3 L TENSOR REMARK 3 L11: 7.8271 L22: 9.7345 REMARK 3 L33: 4.8207 L12: 4.5310 REMARK 3 L13: -0.3473 L23: 5.6437 REMARK 3 S TENSOR REMARK 3 S11: -0.1221 S12: -0.5033 S13: 0.1436 REMARK 3 S21: 1.0460 S22: 0.0800 S23: 0.1448 REMARK 3 S31: 0.9385 S32: 0.3313 S33: 0.0422 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 : A 8 A 30 REMARK 3 ORIGIN FOR THE GROUP (A): 12.6994 -3.7631 30.2615 REMARK 3 T TENSOR REMARK 3 T11: 0.1868 T22: 0.0866 REMARK 3 T33: 0.0399 T12: -0.0032 REMARK 3 T13: 0.0139 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 0.0836 L22: 0.4614 REMARK 3 L33: 3.5910 L12: 0.1605 REMARK 3 L13: -0.3882 L23: -0.5449 REMARK 3 S TENSOR REMARK 3 S11: 0.0211 S12: 0.0179 S13: -0.0197 REMARK 3 S21: 0.0711 S22: -0.0465 S23: -0.0323 REMARK 3 S31: 0.1564 S32: -0.0146 S33: 0.0254 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 : A 31 A 52 REMARK 3 ORIGIN FOR THE GROUP (A): -0.0786 1.9045 33.1028 REMARK 3 T TENSOR REMARK 3 T11: 0.1983 T22: 0.1365 REMARK 3 T33: 0.1078 T12: -0.0592 REMARK 3 T13: 0.0563 T23: -0.0746 REMARK 3 L TENSOR REMARK 3 L11: 1.5662 L22: 1.2212 REMARK 3 L33: 2.7616 L12: -0.8067 REMARK 3 L13: -1.7867 L23: 0.1831 REMARK 3 S TENSOR REMARK 3 S11: 0.1845 S12: 0.1291 S13: -0.1497 REMARK 3 S21: -0.1302 S22: -0.2075 S23: 0.2816 REMARK 3 S31: -0.0882 S32: -0.0757 S33: 0.0230 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 : A 53 A 61 REMARK 3 ORIGIN FOR THE GROUP (A): -3.6039 7.3008 24.2011 REMARK 3 T TENSOR REMARK 3 T11: 0.2156 T22: 0.1716 REMARK 3 T33: 0.1175 T12: -0.0411 REMARK 3 T13: -0.0608 T23: 0.0146 REMARK 3 L TENSOR REMARK 3 L11: 0.6860 L22: 15.2032 REMARK 3 L33: 6.2630 L12: 0.5353 REMARK 3 L13: -0.2513 L23: -9.7481 REMARK 3 S TENSOR REMARK 3 S11: -0.3427 S12: 0.0296 S13: 0.2029 REMARK 3 S21: 0.0314 S22: 0.4356 S23: 0.1876 REMARK 3 S31: -0.0679 S32: -0.2748 S33: -0.0929 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 : A 62 A 80 REMARK 3 ORIGIN FOR THE GROUP (A): 11.4083 3.0724 38.5870 REMARK 3 T TENSOR REMARK 3 T11: 0.2596 T22: 0.0447 REMARK 3 T33: 0.0794 T12: -0.0137 REMARK 3 T13: 0.0606 T23: -0.0323 REMARK 3 L TENSOR REMARK 3 L11: 3.8700 L22: 1.3532 REMARK 3 L33: 0.6877 L12: -0.6090 REMARK 3 L13: 1.5694 L23: -0.0106 REMARK 3 S TENSOR REMARK 3 S11: -0.0806 S12: 0.1214 S13: 0.1054 REMARK 3 S21: 0.2202 S22: -0.0082 S23: 0.0883 REMARK 3 S31: 0.0182 S32: 0.0380 S33: 0.0888 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 : A 81 A 108 REMARK 3 ORIGIN FOR THE GROUP (A): 12.2638 2.4706 27.3876 REMARK 3 T TENSOR REMARK 3 T11: 0.2959 T22: 0.1098 REMARK 3 T33: 0.0636 T12: 0.0031 REMARK 3 T13: 0.0732 T23: 0.0263 REMARK 3 L TENSOR REMARK 3 L11: 0.6255 L22: 0.8180 REMARK 3 L33: 2.2055 L12: -0.6601 REMARK 3 L13: -0.5467 L23: 0.7902 REMARK 3 S TENSOR REMARK 3 S11: 0.0086 S12: 0.0463 S13: -0.0683 REMARK 3 S21: 0.1307 S22: 0.0380 S23: 0.1162 REMARK 3 S31: -0.1321 S32: 0.1819 S33: -0.0466 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 5 REMARK 3 ORIGIN FOR THE GROUP (A): 25.4564 7.8891 19.7223 REMARK 3 T TENSOR REMARK 3 T11: 0.1115 T22: 0.2165 REMARK 3 T33: 0.1418 T12: -0.0707 REMARK 3 T13: -0.0350 T23: -0.0367 REMARK 3 L TENSOR REMARK 3 L11: 3.1517 L22: 1.3322 REMARK 3 L33: 5.7421 L12: 1.9947 REMARK 3 L13: -4.2520 L23: -2.7034 REMARK 3 S TENSOR REMARK 3 S11: 0.0833 S12: -0.1685 S13: -0.1244 REMARK 3 S21: 0.1006 S22: -0.2235 S23: -0.0400 REMARK 3 S31: -0.1144 S32: 0.2432 S33: 0.1402 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 6 B 19 REMARK 3 ORIGIN FOR THE GROUP (A): 18.4858 9.5329 9.1592 REMARK 3 T TENSOR REMARK 3 T11: 0.0764 T22: 0.1160 REMARK 3 T33: 0.1428 T12: -0.0167 REMARK 3 T13: 0.0049 T23: 0.0088 REMARK 3 L TENSOR REMARK 3 L11: 0.0700 L22: 1.7495 REMARK 3 L33: 0.1926 L12: 0.3112 REMARK 3 L13: -0.0870 L23: -0.5586 REMARK 3 S TENSOR REMARK 3 S11: 0.0222 S12: 0.0167 S13: -0.0145 REMARK 3 S21: 0.2286 S22: -0.0603 S23: -0.1285 REMARK 3 S31: -0.0980 S32: 0.0298 S33: 0.0381 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 20 B 48 REMARK 3 ORIGIN FOR THE GROUP (A): 10.2973 4.5857 4.1100 REMARK 3 T TENSOR REMARK 3 T11: 0.0285 T22: 0.1355 REMARK 3 T33: 0.1253 T12: 0.0065 REMARK 3 T13: 0.0244 T23: 0.0066 REMARK 3 L TENSOR REMARK 3 L11: 0.5331 L22: 1.0610 REMARK 3 L33: 0.7868 L12: 0.0019 REMARK 3 L13: -0.0646 L23: 0.3338 REMARK 3 S TENSOR REMARK 3 S11: 0.0569 S12: 0.0480 S13: 0.0834 REMARK 3 S21: 0.1124 S22: -0.0131 S23: 0.1089 REMARK 3 S31: -0.0514 S32: -0.1197 S33: -0.0438 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 49 B 60 REMARK 3 ORIGIN FOR THE GROUP (A): 0.5576 -4.4980 9.2141 REMARK 3 T TENSOR REMARK 3 T11: 0.1457 T22: 0.2229 REMARK 3 T33: 0.2061 T12: -0.1156 REMARK 3 T13: 0.0753 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 3.1264 L22: 1.1434 REMARK 3 L33: 2.8473 L12: -1.3585 REMARK 3 L13: 2.5321 L23: -1.7638 REMARK 3 S TENSOR REMARK 3 S11: 0.3315 S12: -0.2267 S13: -0.1352 REMARK 3 S21: 0.0747 S22: 0.0426 S23: 0.2844 REMARK 3 S31: 0.0032 S32: -0.1067 S33: -0.3741 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 61 B 88 REMARK 3 ORIGIN FOR THE GROUP (A): 14.9135 1.1484 2.3340 REMARK 3 T TENSOR REMARK 3 T11: 0.0167 T22: 0.1300 REMARK 3 T33: 0.1403 T12: 0.0089 REMARK 3 T13: 0.0163 T23: 0.0119 REMARK 3 L TENSOR REMARK 3 L11: 0.9978 L22: 0.6740 REMARK 3 L33: 0.3335 L12: -0.0871 REMARK 3 L13: -0.4469 L23: 0.3219 REMARK 3 S TENSOR REMARK 3 S11: 0.0259 S12: 0.0075 S13: -0.1115 REMARK 3 S21: 0.0028 S22: -0.0407 S23: -0.0134 REMARK 3 S31: -0.0185 S32: -0.0535 S33: 0.0148 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 89 B 108 REMARK 3 ORIGIN FOR THE GROUP (A): 19.6617 1.1605 14.4333 REMARK 3 T TENSOR REMARK 3 T11: 0.0718 T22: 0.1426 REMARK 3 T33: 0.0931 T12: 0.0005 REMARK 3 T13: 0.0289 T23: -0.0022 REMARK 3 L TENSOR REMARK 3 L11: 0.3046 L22: 1.1299 REMARK 3 L33: 0.5992 L12: 0.0344 REMARK 3 L13: -0.1248 L23: 0.5181 REMARK 3 S TENSOR REMARK 3 S11: 0.0384 S12: -0.1199 S13: 0.0100 REMARK 3 S21: 0.0420 S22: 0.0176 S23: -0.0043 REMARK 3 S31: 0.0944 S32: 0.0950 S33: -0.0560 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6S1V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1292102879. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR, SI REMARK 200 -111 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30408 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 48.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.650 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.56 REMARK 200 R MERGE FOR SHELL (I) : 0.82600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.370 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6S1U, CHAIN A REMARK 200 REMARK 200 REMARK: PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 5.0 MG/ML PROTEIN REMARK 280 WITH 1.4-FOLD MOLAR EXCESS (RELATIVE TO DIMERIC PROTEIN) OF PRO- REMARK 280 0A1-VAL-PSA-ALA-MET-THR (INHIBITOR), 5 MM TCEP, 10 MM TRIS REMARK 280 BUFFER PH 7.4; RESERVOIR SOLUTION: 0.1 M SODIUM CITRATE BUFFER, REMARK 280 25% PROPAN-2-OL, 5 MM TCEP;, PH 5.6, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 292K 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 14.75200 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, I 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 54 REMARK 465 ILE A 55 REMARK 465 GLY A 56 REMARK 465 GLN A 57 REMARK 465 SER A 58 REMARK 465 ASN A 109 REMARK 465 ASP A 110 REMARK 465 ILE A 111 REMARK 465 VAL A 112 REMARK 465 THR A 113 REMARK 465 ALA A 114 REMARK 465 GLY B 54 REMARK 465 ILE B 55 REMARK 465 GLY B 56 REMARK 465 ASN B 109 REMARK 465 ASP B 110 REMARK 465 ILE B 111 REMARK 465 VAL B 112 REMARK 465 THR B 113 REMARK 465 ALA B 114 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 53 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 53 CG CD NE CZ NH1 NH2 REMARK 470 PRO I 1 CG CD 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 PSA I 4 CA - C - N ANGL. DEV. = 16.7 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 ASP A 17 58.03 36.06 REMARK 500 ASP B 17 -123.19 40.35 REMARK 500 ASN B 60 42.65 -141.81 REMARK 500 MET I 6 139.40 -173.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SQF RELATED DB: PDB REMARK 900 CONTAINS THE SAME PROTEIN IN MONOMERIC STATE. REMARK 900 RELATED ID: 3HVP RELATED DB: PDB REMARK 900 CONTAINS HIV-1 PROTEASE IN APO FORM. REMARK 900 RELATED ID: 4HVP RELATED DB: PDB REMARK 900 CONTAINS HIV-1 PROTEASE INHIBITOR COMPLEX. REMARK 900 RELATED ID: 1IVP RELATED DB: PDB REMARK 900 CONTAINS HIV-2 PROTEASE INHIBITOR COMPLEX. REMARK 900 RELATED ID: 1AZ5 RELATED DB: PDB REMARK 900 CONTAINS SIV PROTEASE APO FORM. REMARK 900 RELATED ID: 2RSP RELATED DB: PDB REMARK 900 CONTAINS RSV PROTEASE APO FORM. REMARK 900 RELATED ID: 1BAI RELATED DB: PDB REMARK 900 CONTAINS RSV PROTEASE INHIBITOR COMPLEX. REMARK 900 RELATED ID: 4FIV RELATED DB: PDB REMARK 900 CONTAINS FIV PROTEASE INHIBITOR COMPLEX. REMARK 900 RELATED ID: 2FMB RELATED DB: PDB REMARK 900 CONTAINS EIAV PROTEASE INHIBITOR COMPLEX. REMARK 900 RELATED ID: 3LIY RELATED DB: PDB REMARK 900 CONTAINS HTLV PROTEASE INHIBITOR COMPLEX. REMARK 900 RELATED ID: 3SLZ RELATED DB: PDB REMARK 900 CONTAINS XMRV PROTEASE INHIBITOR COMPLEX. DBREF 6S1V A 1 114 UNP P07572 POL_MPMV 760 873 DBREF 6S1V B 1 114 UNP P07572 POL_MPMV 760 873 DBREF 6S1V I 1 7 PDB 6S1V 6S1V 1 7 SEQADV 6S1V ASN A 26 UNP P07572 ASP 785 ENGINEERED MUTATION SEQADV 6S1V ASN B 26 UNP P07572 ASP 785 ENGINEERED MUTATION SEQRES 1 A 114 TRP VAL GLN PRO ILE THR CYS GLN LYS PRO SER LEU THR SEQRES 2 A 114 LEU TRP LEU ASP ASP LYS MET PHE THR GLY LEU ILE ASN SEQRES 3 A 114 THR GLY ALA ASP VAL THR ILE ILE LYS LEU GLU ASP TRP SEQRES 4 A 114 PRO PRO ASN TRP PRO ILE THR ASP THR LEU THR ASN LEU SEQRES 5 A 114 ARG GLY ILE GLY GLN SER ASN ASN PRO LYS GLN SER SER SEQRES 6 A 114 LYS TYR LEU THR TRP ARG ASP LYS GLU ASN ASN SER GLY SEQRES 7 A 114 LEU ILE LYS PRO PHE VAL ILE PRO ASN LEU PRO VAL ASN SEQRES 8 A 114 LEU TRP GLY ARG ASP LEU LEU SER GLN MET LYS ILE MET SEQRES 9 A 114 MET CYS SER PRO ASN ASP ILE VAL THR ALA SEQRES 1 B 114 TRP VAL GLN PRO ILE THR CYS GLN LYS PRO SER LEU THR SEQRES 2 B 114 LEU TRP LEU ASP ASP LYS MET PHE THR GLY LEU ILE ASN SEQRES 3 B 114 THR GLY ALA ASP VAL THR ILE ILE LYS LEU GLU ASP TRP SEQRES 4 B 114 PRO PRO ASN TRP PRO ILE THR ASP THR LEU THR ASN LEU SEQRES 5 B 114 ARG GLY ILE GLY GLN SER ASN ASN PRO LYS GLN SER SER SEQRES 6 B 114 LYS TYR LEU THR TRP ARG ASP LYS GLU ASN ASN SER GLY SEQRES 7 B 114 LEU ILE LYS PRO PHE VAL ILE PRO ASN LEU PRO VAL ASN SEQRES 8 B 114 LEU TRP GLY ARG ASP LEU LEU SER GLN MET LYS ILE MET SEQRES 9 B 114 MET CYS SER PRO ASN ASP ILE VAL THR ALA SEQRES 1 I 7 PRO 0A1 VAL PSA ALA MET THR HET 0A1 I 2 13 HET PSA I 4 14 HETNAM 0A1 O-METHYL-L-TYROSINE HETNAM PSA 3-HYDROXY-4-AMINO-5-PHENYLPENTANOIC ACID FORMUL 3 0A1 C10 H13 N O3 FORMUL 3 PSA C11 H15 N O3 FORMUL 4 HOH *157(H2 O) HELIX 1 AA1 GLU A 37 TRP A 39 5 3 HELIX 2 AA2 GLY A 94 MET A 101 1 8 HELIX 3 AA3 GLU B 37 TRP B 39 5 3 HELIX 4 AA4 GLY B 94 MET B 101 1 8 SHEET 1 AA1 4 VAL A 2 PRO A 4 0 SHEET 2 AA1 4 MET B 104 CYS B 106 -1 O MET B 105 N GLN A 3 SHEET 3 AA1 4 MET A 104 CYS A 106 -1 N MET A 104 O CYS B 106 SHEET 4 AA1 4 VAL B 2 PRO B 4 -1 O GLN B 3 N MET A 105 SHEET 1 AA2 5 SER A 77 ILE A 80 0 SHEET 2 AA2 5 LEU A 68 ARG A 71 -1 N LEU A 68 O ILE A 80 SHEET 3 AA2 5 SER A 11 LEU A 16 -1 N TRP A 15 O ARG A 71 SHEET 4 AA2 5 LYS A 19 ILE A 25 -1 O PHE A 21 N LEU A 14 SHEET 5 AA2 5 LEU A 92 TRP A 93 1 O TRP A 93 N LEU A 24 SHEET 1 AA3 4 ILE A 33 LYS A 35 0 SHEET 2 AA3 4 PHE A 83 ILE A 85 1 O PHE A 83 N ILE A 34 SHEET 3 AA3 4 LYS A 62 SER A 64 -1 N LYS A 62 O VAL A 84 SHEET 4 AA3 4 ILE A 45 THR A 46 -1 N THR A 46 O GLN A 63 SHEET 1 AA4 5 SER B 77 ILE B 80 0 SHEET 2 AA4 5 LEU B 68 ARG B 71 -1 N LEU B 68 O ILE B 80 SHEET 3 AA4 5 SER B 11 LEU B 16 -1 N TRP B 15 O ARG B 71 SHEET 4 AA4 5 LYS B 19 ILE B 25 -1 O PHE B 21 N LEU B 14 SHEET 5 AA4 5 ASN B 91 TRP B 93 1 O TRP B 93 N LEU B 24 SHEET 1 AA5 4 ILE B 33 LYS B 35 0 SHEET 2 AA5 4 PHE B 83 ILE B 85 1 O PHE B 83 N ILE B 34 SHEET 3 AA5 4 LYS B 62 SER B 64 -1 N LYS B 62 O VAL B 84 SHEET 4 AA5 4 ILE B 45 ASP B 47 -1 N THR B 46 O GLN B 63 LINK C PRO I 1 N 0A1 I 2 1555 1555 1.34 LINK C 0A1 I 2 N VAL I 3 1555 1555 1.34 LINK C VAL I 3 N PSA I 4 1555 1555 1.33 LINK C PSA I 4 N ALA I 5 1555 1555 1.32 CRYST1 49.947 29.504 85.390 90.00 101.71 90.00 P 1 21 1 4 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 0.020021 0.000000 0.004149 0.00000 SCALE2 0.000000 0.033894 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011960 0.00000