HEADER HYDROLASE/HYDROLASE INHIBITOR 02-FEB-12 4DJQ TITLE CRYSTAL STRUCTURE OF WILD-TYPE HIV-1 PROTEASE IN COMPLEX WITH MKP86 COMPND MOL_ID: 1; COMPND 2 MOLECULE: POL POLYPROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-99; COMPND 5 SYNONYM: HIV-1 PROTEASE; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 STRAIN: SF2; SOURCE 5 GENE: GAG-POL, POL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TAP56; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PXC35 KEYWDS HIV-1 PROTEASE, DRUG RESISTANCE, DRUG DESIGN, PROTEASE INHIBITORS, KEYWDS 2 AIDS, ASPARTYL PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.A.SCHIFFER,M.N.L.NALAM REVDAT 4 28-FEB-24 4DJQ 1 REMARK SEQADV REVDAT 3 15-NOV-17 4DJQ 1 REMARK REVDAT 2 02-JAN-13 4DJQ 1 JRNL REVDAT 1 01-AUG-12 4DJQ 0 JRNL AUTH M.K.PARAI,D.J.HUGGINS,H.CAO,M.N.NALAM,A.ALI,C.A.SCHIFFER, JRNL AUTH 2 B.TIDOR,T.M.RANA JRNL TITL DESIGN, SYNTHESIS, AND BIOLOGICAL AND STRUCTURAL EVALUATIONS JRNL TITL 2 OF NOVEL HIV-1 PROTEASE INHIBITORS TO COMBAT DRUG JRNL TITL 3 RESISTANCE. JRNL REF J.MED.CHEM. V. 55 6328 2012 JRNL REFN ISSN 0022-2623 JRNL PMID 22708897 JRNL DOI 10.1021/JM300238H REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 36051 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 : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1809 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2504 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 131 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1498 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 196 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.39000 REMARK 3 B22 (A**2) : -0.17000 REMARK 3 B33 (A**2) : 0.56000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.066 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.067 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.276 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1639 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1103 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2241 ; 1.368 ; 2.017 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2726 ; 0.791 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 210 ; 6.164 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 56 ;39.969 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 278 ;10.798 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;13.672 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 264 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1799 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 295 ; 0.001 ; 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): 1020 ; 0.546 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 426 ; 0.144 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1667 ; 0.956 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 619 ; 1.534 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 574 ; 2.468 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 20 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 5 REMARK 3 RESIDUE RANGE : A 94 A 99 REMARK 3 RESIDUE RANGE : A 6 A 10 REMARK 3 ORIGIN FOR THE GROUP (A): -4.3187 3.1806 -29.5924 REMARK 3 T TENSOR REMARK 3 T11: 0.1090 T22: 0.0907 REMARK 3 T33: 0.0027 T12: -0.0318 REMARK 3 T13: -0.0093 T23: -0.0005 REMARK 3 L TENSOR REMARK 3 L11: 2.6417 L22: 1.6891 REMARK 3 L33: 2.2267 L12: 0.2444 REMARK 3 L13: -0.0560 L23: -0.5477 REMARK 3 S TENSOR REMARK 3 S11: -0.0864 S12: 0.2611 S13: 0.0018 REMARK 3 S21: -0.2512 S22: 0.0675 S23: -0.0194 REMARK 3 S31: 0.1461 S32: -0.0257 S33: 0.0190 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 5 REMARK 3 RESIDUE RANGE : B 94 B 99 REMARK 3 RESIDUE RANGE : B 6 B 10 REMARK 3 ORIGIN FOR THE GROUP (A): -5.7881 11.6384 -22.9265 REMARK 3 T TENSOR REMARK 3 T11: 0.0680 T22: 0.0615 REMARK 3 T33: 0.0669 T12: 0.0014 REMARK 3 T13: -0.0182 T23: 0.0114 REMARK 3 L TENSOR REMARK 3 L11: 1.5326 L22: 2.5947 REMARK 3 L33: 2.2952 L12: 1.3397 REMARK 3 L13: -0.3181 L23: -0.4367 REMARK 3 S TENSOR REMARK 3 S11: -0.0324 S12: 0.0768 S13: 0.2096 REMARK 3 S21: -0.1267 S22: 0.0918 S23: 0.2442 REMARK 3 S31: -0.1353 S32: -0.0393 S33: -0.0594 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 21 A 32 REMARK 3 ORIGIN FOR THE GROUP (A): 1.0442 1.7547 -18.2130 REMARK 3 T TENSOR REMARK 3 T11: 0.0637 T22: 0.0699 REMARK 3 T33: 0.0397 T12: -0.0063 REMARK 3 T13: 0.0059 T23: 0.0092 REMARK 3 L TENSOR REMARK 3 L11: 3.3651 L22: 3.3699 REMARK 3 L33: 0.7314 L12: -0.9389 REMARK 3 L13: -0.1043 L23: -1.2944 REMARK 3 S TENSOR REMARK 3 S11: -0.0218 S12: -0.0434 S13: 0.0114 REMARK 3 S21: -0.0358 S22: -0.0740 S23: -0.1341 REMARK 3 S31: 0.0560 S32: 0.0508 S33: 0.0958 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 : B 21 B 32 REMARK 3 ORIGIN FOR THE GROUP (A): -11.5678 1.2791 -19.2653 REMARK 3 T TENSOR REMARK 3 T11: 0.0648 T22: 0.0646 REMARK 3 T33: 0.0791 T12: -0.0129 REMARK 3 T13: -0.0095 T23: 0.0128 REMARK 3 L TENSOR REMARK 3 L11: 2.2786 L22: 2.2226 REMARK 3 L33: 1.2938 L12: 0.5717 REMARK 3 L13: -1.1225 L23: -0.8574 REMARK 3 S TENSOR REMARK 3 S11: -0.0277 S12: -0.0120 S13: 0.1251 REMARK 3 S21: -0.0179 S22: 0.1333 S23: 0.2381 REMARK 3 S31: 0.0644 S32: 0.0044 S33: -0.1056 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 11 A 20 REMARK 3 ORIGIN FOR THE GROUP (A): 14.1061 -2.1098 -23.2521 REMARK 3 T TENSOR REMARK 3 T11: 0.2685 T22: 0.0987 REMARK 3 T33: 0.4222 T12: 0.0016 REMARK 3 T13: 0.2820 T23: 0.0842 REMARK 3 L TENSOR REMARK 3 L11: 4.0376 L22: 7.3454 REMARK 3 L33: 2.6013 L12: 1.1687 REMARK 3 L13: 3.1852 L23: 0.3824 REMARK 3 S TENSOR REMARK 3 S11: 0.2439 S12: 0.1426 S13: 0.1473 REMARK 3 S21: -0.6306 S22: -0.4794 S23: -1.4963 REMARK 3 S31: 0.3757 S32: 0.1078 S33: 0.2355 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 : B 11 B 20 REMARK 3 ORIGIN FOR THE GROUP (A): -23.9742 7.2440 -17.7663 REMARK 3 T TENSOR REMARK 3 T11: 0.0366 T22: 0.0837 REMARK 3 T33: 0.2237 T12: 0.0048 REMARK 3 T13: 0.0263 T23: 0.0157 REMARK 3 L TENSOR REMARK 3 L11: 7.4503 L22: 3.4842 REMARK 3 L33: 4.2924 L12: 3.1768 REMARK 3 L13: 1.3440 L23: -0.9771 REMARK 3 S TENSOR REMARK 3 S11: 0.2059 S12: -0.1556 S13: 0.4429 REMARK 3 S21: 0.2763 S22: 0.0559 S23: 0.4570 REMARK 3 S31: 0.0452 S32: -0.4599 S33: -0.2618 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 : A 33 A 43 REMARK 3 ORIGIN FOR THE GROUP (A): 14.0964 -2.3998 -10.0515 REMARK 3 T TENSOR REMARK 3 T11: 0.0789 T22: 0.1453 REMARK 3 T33: 0.1066 T12: 0.0203 REMARK 3 T13: -0.0183 T23: 0.0681 REMARK 3 L TENSOR REMARK 3 L11: 3.7035 L22: 1.6460 REMARK 3 L33: 3.7966 L12: -0.0887 REMARK 3 L13: -0.8709 L23: 2.1856 REMARK 3 S TENSOR REMARK 3 S11: 0.0010 S12: -0.1893 S13: -0.2270 REMARK 3 S21: 0.0788 S22: 0.0922 S23: -0.2035 REMARK 3 S31: 0.2118 S32: 0.4154 S33: -0.0931 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 33 B 43 REMARK 3 ORIGIN FOR THE GROUP (A): -24.9708 -5.2997 -13.0717 REMARK 3 T TENSOR REMARK 3 T11: 0.0708 T22: 0.1557 REMARK 3 T33: 0.0572 T12: 0.0063 REMARK 3 T13: -0.0063 T23: 0.0710 REMARK 3 L TENSOR REMARK 3 L11: 7.2434 L22: 6.8851 REMARK 3 L33: 4.0394 L12: 1.2296 REMARK 3 L13: 1.2765 L23: 3.6674 REMARK 3 S TENSOR REMARK 3 S11: 0.1158 S12: -0.3288 S13: 0.0811 REMARK 3 S21: 0.0740 S22: -0.0865 S23: 0.2863 REMARK 3 S31: -0.1324 S32: -0.5027 S33: -0.0293 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 : A 44 A 57 REMARK 3 ORIGIN FOR THE GROUP (A): 2.0800 -1.5472 -4.1344 REMARK 3 T TENSOR REMARK 3 T11: 0.0962 T22: 0.0835 REMARK 3 T33: 0.0445 T12: -0.0166 REMARK 3 T13: 0.0012 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 7.4359 L22: 1.9892 REMARK 3 L33: 2.8649 L12: 1.2307 REMARK 3 L13: 1.7164 L23: 0.5051 REMARK 3 S TENSOR REMARK 3 S11: -0.0409 S12: -0.1713 S13: 0.2409 REMARK 3 S21: 0.0845 S22: -0.0419 S23: 0.0536 REMARK 3 S31: -0.0444 S32: 0.0548 S33: 0.0828 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 44 B 57 REMARK 3 ORIGIN FOR THE GROUP (A): -12.9504 -10.5147 -11.3816 REMARK 3 T TENSOR REMARK 3 T11: 0.0920 T22: 0.0778 REMARK 3 T33: 0.0766 T12: 0.0027 REMARK 3 T13: 0.0008 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 6.0826 L22: 2.7525 REMARK 3 L33: 1.4591 L12: 2.8780 REMARK 3 L13: 0.7728 L23: -1.0049 REMARK 3 S TENSOR REMARK 3 S11: 0.0782 S12: -0.1181 S13: 0.1739 REMARK 3 S21: 0.0329 S22: -0.0343 S23: 0.1693 REMARK 3 S31: 0.0288 S32: -0.0165 S33: -0.0439 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 : A 77 A 85 REMARK 3 ORIGIN FOR THE GROUP (A): 3.5429 -4.6085 -14.1503 REMARK 3 T TENSOR REMARK 3 T11: 0.0828 T22: 0.0770 REMARK 3 T33: 0.0770 T12: 0.0047 REMARK 3 T13: 0.0227 T23: 0.0262 REMARK 3 L TENSOR REMARK 3 L11: 0.7467 L22: 2.6550 REMARK 3 L33: 3.4081 L12: -1.3163 REMARK 3 L13: 0.9969 L23: -0.9795 REMARK 3 S TENSOR REMARK 3 S11: 0.0240 S12: 0.0179 S13: -0.0840 REMARK 3 S21: -0.0119 S22: -0.0722 S23: 0.1800 REMARK 3 S31: 0.2305 S32: 0.0456 S33: 0.0481 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 77 B 85 REMARK 3 ORIGIN FOR THE GROUP (A): -14.8437 -0.2002 -11.9163 REMARK 3 T TENSOR REMARK 3 T11: 0.1339 T22: 0.0843 REMARK 3 T33: 0.0965 T12: -0.0061 REMARK 3 T13: 0.0496 T23: 0.0159 REMARK 3 L TENSOR REMARK 3 L11: 4.7341 L22: 4.4585 REMARK 3 L33: 3.8787 L12: 4.0072 REMARK 3 L13: -4.0542 L23: -2.9211 REMARK 3 S TENSOR REMARK 3 S11: 0.3573 S12: -0.2457 S13: 0.2080 REMARK 3 S21: 0.3129 S22: -0.1539 S23: 0.2718 REMARK 3 S31: -0.4311 S32: 0.1962 S33: -0.2034 REMARK 3 REMARK 3 TLS GROUP : 13 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 86 A 93 REMARK 3 ORIGIN FOR THE GROUP (A): 3.4015 10.0074 -19.3409 REMARK 3 T TENSOR REMARK 3 T11: 0.0595 T22: 0.0673 REMARK 3 T33: 0.0629 T12: -0.0092 REMARK 3 T13: 0.0003 T23: 0.0021 REMARK 3 L TENSOR REMARK 3 L11: 1.0144 L22: 2.7598 REMARK 3 L33: 1.6940 L12: 0.7840 REMARK 3 L13: 0.5648 L23: -0.3732 REMARK 3 S TENSOR REMARK 3 S11: -0.0146 S12: -0.0030 S13: 0.0285 REMARK 3 S21: 0.0072 S22: -0.0431 S23: -0.1404 REMARK 3 S31: -0.0580 S32: 0.0898 S33: 0.0577 REMARK 3 REMARK 3 TLS GROUP : 14 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 86 B 93 REMARK 3 ORIGIN FOR THE GROUP (A): -13.4415 -0.1315 -27.1735 REMARK 3 T TENSOR REMARK 3 T11: 0.1423 T22: 0.1421 REMARK 3 T33: 0.0860 T12: -0.0670 REMARK 3 T13: -0.0659 T23: 0.0765 REMARK 3 L TENSOR REMARK 3 L11: 7.6117 L22: 2.3973 REMARK 3 L33: 0.0481 L12: 4.2600 REMARK 3 L13: 0.5546 L23: 0.3018 REMARK 3 S TENSOR REMARK 3 S11: -0.4631 S12: 0.6744 S13: 0.2199 REMARK 3 S21: -0.3046 S22: 0.4334 S23: 0.1533 REMARK 3 S31: -0.0074 S32: 0.0389 S33: 0.0297 REMARK 3 REMARK 3 TLS GROUP : 15 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 58 A 62 REMARK 3 ORIGIN FOR THE GROUP (A): 13.4137 6.3323 -10.2683 REMARK 3 T TENSOR REMARK 3 T11: 0.0520 T22: 0.1517 REMARK 3 T33: 0.2083 T12: -0.0497 REMARK 3 T13: -0.0699 T23: 0.0645 REMARK 3 L TENSOR REMARK 3 L11: 1.1036 L22: 7.1682 REMARK 3 L33: 13.7141 L12: 2.8043 REMARK 3 L13: -2.3652 L23: -5.5260 REMARK 3 S TENSOR REMARK 3 S11: 0.1231 S12: -0.1093 S13: -0.0010 REMARK 3 S21: 0.2969 S22: -0.2705 S23: -0.0492 REMARK 3 S31: -0.2654 S32: 0.2952 S33: 0.1474 REMARK 3 REMARK 3 TLS GROUP : 16 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 58 B 62 REMARK 3 ORIGIN FOR THE GROUP (A): -23.7565 -7.8001 -21.3352 REMARK 3 T TENSOR REMARK 3 T11: 0.0538 T22: 0.0764 REMARK 3 T33: 0.1717 T12: -0.0498 REMARK 3 T13: -0.0403 T23: 0.0562 REMARK 3 L TENSOR REMARK 3 L11: 7.2172 L22: 9.9453 REMARK 3 L33: 9.3434 L12: -6.0153 REMARK 3 L13: 5.2182 L23: -4.5245 REMARK 3 S TENSOR REMARK 3 S11: 0.2059 S12: 0.1746 S13: -0.2885 REMARK 3 S21: -0.3967 S22: -0.0046 S23: 0.3145 REMARK 3 S31: 0.3291 S32: 0.0170 S33: -0.2013 REMARK 3 REMARK 3 TLS GROUP : 17 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 63 A 68 REMARK 3 ORIGIN FOR THE GROUP (A): 12.4365 5.0828 -23.9834 REMARK 3 T TENSOR REMARK 3 T11: 0.0604 T22: 0.0637 REMARK 3 T33: 0.1537 T12: 0.0330 REMARK 3 T13: 0.0761 T23: 0.0482 REMARK 3 L TENSOR REMARK 3 L11: 6.1709 L22: 6.9192 REMARK 3 L33: 11.7597 L12: 1.4881 REMARK 3 L13: 3.4248 L23: -0.1120 REMARK 3 S TENSOR REMARK 3 S11: -0.0930 S12: 0.1519 S13: -0.4330 REMARK 3 S21: -0.4741 S22: -0.0870 S23: -0.4809 REMARK 3 S31: 0.0724 S32: 0.3027 S33: 0.1800 REMARK 3 REMARK 3 TLS GROUP : 18 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 63 B 68 REMARK 3 ORIGIN FOR THE GROUP (A): -22.3764 5.7694 -24.7208 REMARK 3 T TENSOR REMARK 3 T11: 0.1903 T22: 0.1009 REMARK 3 T33: 0.1475 T12: -0.0562 REMARK 3 T13: -0.1325 T23: 0.0708 REMARK 3 L TENSOR REMARK 3 L11: 11.1542 L22: 14.5758 REMARK 3 L33: 2.6252 L12: 8.3743 REMARK 3 L13: -2.8293 L23: 1.4101 REMARK 3 S TENSOR REMARK 3 S11: 0.0372 S12: -0.2878 S13: 0.3899 REMARK 3 S21: -0.0941 S22: -0.1716 S23: 0.4120 REMARK 3 S31: -0.3292 S32: 0.1386 S33: 0.1344 REMARK 3 REMARK 3 TLS GROUP : 19 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 69 A 76 REMARK 3 ORIGIN FOR THE GROUP (A): 10.8988 7.7399 -19.4361 REMARK 3 T TENSOR REMARK 3 T11: 0.0563 T22: 0.0651 REMARK 3 T33: 0.1081 T12: -0.0058 REMARK 3 T13: -0.0199 T23: 0.0356 REMARK 3 L TENSOR REMARK 3 L11: 1.6735 L22: 3.1118 REMARK 3 L33: 4.0303 L12: 0.9378 REMARK 3 L13: -1.0253 L23: -1.5175 REMARK 3 S TENSOR REMARK 3 S11: -0.0079 S12: -0.0416 S13: -0.0047 REMARK 3 S21: -0.1324 S22: -0.1730 S23: -0.3707 REMARK 3 S31: -0.0650 S32: 0.2107 S33: 0.1809 REMARK 3 REMARK 3 TLS GROUP : 20 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 69 B 76 REMARK 3 ORIGIN FOR THE GROUP (A): -21.2346 0.4784 -25.6050 REMARK 3 T TENSOR REMARK 3 T11: 0.0690 T22: 0.0818 REMARK 3 T33: 0.1210 T12: -0.0489 REMARK 3 T13: -0.0431 T23: 0.0603 REMARK 3 L TENSOR REMARK 3 L11: 0.9889 L22: 2.3889 REMARK 3 L33: 3.1054 L12: -0.1124 REMARK 3 L13: 1.6537 L23: -1.0817 REMARK 3 S TENSOR REMARK 3 S11: -0.1102 S12: 0.0805 S13: 0.0361 REMARK 3 S21: -0.0149 S22: 0.1531 S23: 0.3309 REMARK 3 S31: -0.1934 S32: 0.0835 S33: -0.0429 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 4DJQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070415. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-10 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 : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36239 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.35200 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 126MM PHOSPHATE BUFFER, 63MM SODIUM REMARK 280 CITRATE, 24-29% AMMONIUM SULFATE, PH 6.2, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 25.35550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.90750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.96500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.90750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.35550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.96500 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 LYS A 7 CG CD CE NZ REMARK 470 LYS A 41 CG CD CE NZ REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 LYS B 41 CG CD CE NZ REMARK 470 LYS B 43 CG CD CE NZ REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE M86 A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DJO RELATED DB: PDB REMARK 900 RELATED ID: 4DJP RELATED DB: PDB REMARK 900 RELATED ID: 4DJR RELATED DB: PDB DBREF 4DJQ A 1 99 UNP Q90K99 Q90K99_9HIV1 1 99 DBREF 4DJQ B 1 99 UNP Q90K99 Q90K99_9HIV1 1 99 SEQADV 4DJQ LYS A 7 UNP Q90K99 GLN 7 ENGINEERED MUTATION SEQADV 4DJQ LYS B 7 UNP Q90K99 GLN 7 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 A 99 ARG ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 A 99 GLY ALA ASP ASP THR VAL LEU GLU GLU MET ASN LEU PRO SEQRES 4 A 99 GLY LYS TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 A 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE PRO ILE GLU SEQRES 6 A 99 ILE CYS GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 A 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 A 99 GLN ILE GLY CYS THR LEU ASN PHE SEQRES 1 B 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 B 99 ARG ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 B 99 GLY ALA ASP ASP THR VAL LEU GLU GLU MET ASN LEU PRO SEQRES 4 B 99 GLY LYS TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 B 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE PRO ILE GLU SEQRES 6 B 99 ILE CYS GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 B 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 B 99 GLN ILE GLY CYS THR LEU ASN PHE HET M86 A 200 40 HET PO4 B 101 5 HET PO4 B 102 5 HETNAM M86 2-(2-OXOIMIDAZOLIDIN-1-YL)ETHYL [(2S,3R)-3-HYDROXY-4- HETNAM 2 M86 {[(4-METHOXYPHENYL)SULFONYL][(2S)-2- HETNAM 3 M86 METHYLBUTYL]AMINO}-1-PHENYLBUTAN-2-YL]CARBAMATE HETNAM PO4 PHOSPHATE ION FORMUL 3 M86 C28 H40 N4 O7 S FORMUL 4 PO4 2(O4 P 3-) FORMUL 6 HOH *196(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLY B 86 THR B 91 1 6 SHEET 1 A 4 GLN A 2 ILE A 3 0 SHEET 2 A 4 THR B 96 ASN B 98 -1 O LEU B 97 N ILE A 3 SHEET 3 A 4 THR A 96 ASN A 98 -1 N ASN A 98 O THR B 96 SHEET 4 A 4 GLN B 2 ILE B 3 -1 O ILE B 3 N 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 HIS A 69 VAL A 77 -1 O HIS A 69 N ILE A 66 SHEET 4 B 8 VAL A 32 LEU A 33 1 N LEU A 33 O LEU A 76 SHEET 5 B 8 ILE A 84 ILE A 85 -1 O ILE A 84 N VAL A 32 SHEET 6 B 8 LEU A 19 LEU A 24 1 N LEU A 23 O ILE A 85 SHEET 7 B 8 LEU A 10 ARG A 14 -1 N ILE A 13 O LYS A 20 SHEET 8 B 8 GLY A 52 ILE A 66 -1 O GLU A 65 N ARG A 14 SHEET 1 C 8 LYS B 43 GLY B 49 0 SHEET 2 C 8 GLY B 52 ILE B 66 -1 O GLN B 58 N LYS B 43 SHEET 3 C 8 HIS B 69 VAL B 77 -1 O HIS B 69 N ILE B 66 SHEET 4 C 8 THR B 31 LEU B 33 1 N LEU B 33 O LEU B 76 SHEET 5 C 8 ASN B 83 ILE B 85 -1 O ILE B 84 N VAL B 32 SHEET 6 C 8 LEU B 19 LEU B 24 1 N LEU B 23 O ILE B 85 SHEET 7 C 8 LEU B 10 ARG B 14 -1 N ILE B 13 O LYS B 20 SHEET 8 C 8 GLY B 52 ILE B 66 -1 O GLU B 65 N ARG B 14 SITE 1 AC1 18 ASP A 25 GLY A 27 ALA A 28 ASP A 29 SITE 2 AC1 18 GLY A 48 ILE A 50 HOH A 301 HOH A 392 SITE 3 AC1 18 ARG B 8 ASP B 25 GLY B 27 ALA B 28 SITE 4 AC1 18 ASP B 30 GLY B 48 GLY B 49 VAL B 82 SITE 5 AC1 18 ILE B 84 HOH B 265 SITE 1 AC2 6 GLY A 68 HIS A 69 LYS A 70 HOH A 338 SITE 2 AC2 6 PRO B 1 LYS B 55 SITE 1 AC3 7 ARG A 14 GLY A 16 GLY A 17 HOH A 343 SITE 2 AC3 7 GLY B 16 HOH B 232 HOH B 236 CRYST1 50.711 57.930 61.815 90.00 90.00 90.00 P 21 21 21 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 0.019720 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017262 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016177 0.00000