PDB Short entry for 3NX0 HEADER HYDROLASE INHIBITOR 12-JUL-10 3NX0 TITLE HINGE-LOOP MUTATION CAN BE USED TO CONTROL 3D DOMAIN SWAPPING AND TITLE 2 AMYLOIDOGENESIS OF HUMAN CYSTATIN C CAVEAT 3NX0 CHIRALITY ERROR AT CA ATOM OF ASN A57 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTATIN-C; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 27-146; COMPND 5 SYNONYM: CYSTATIN-3, NEUROENDOCRINE BASIC POLYPEPTIDE, GAMMA-TRACE, COMPND 6 POST-GAMMA-GLOBULIN; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CST3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: C41(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PHD313 KEYWDS CYSTEINE PROTEASE INHIBITOR, 3D DOMAIN SWAPPING, PROTEIN ENGINEERING, KEYWDS 2 PROTEIN OLIGOMERIZATION, PROTEIN AGGREGATION, AMYLOID, HYDROLASE KEYWDS 3 INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR M.ORLIKOWSKA,E.JANKOWSKA,R.KOLODZIEJCZYK,M.JASKOLSKI,A.SZYMANSKA REVDAT 3 02-MAR-11 3NX0 1 JRNL REVDAT 2 15-DEC-10 3NX0 1 CAVEAT REVDAT 1 01-DEC-10 3NX0 0 JRNL AUTH M.ORLIKOWSKA,E.JANKOWSKA,R.KOLODZIEJCZYK,M.JASKOLSKI, JRNL AUTH 2 A.SZYMANSKA JRNL TITL HINGE-LOOP MUTATION CAN BE USED TO CONTROL 3D DOMAIN JRNL TITL 2 SWAPPING AND AMYLOIDOGENESIS OF HUMAN CYSTATIN C. JRNL REF J.STRUCT.BIOL. V. 173 406 2011 JRNL REFN ISSN 1047-8477 JRNL PMID 21074623 JRNL DOI 10.1016/J.JSB.2010.11.009 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 18703 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 998 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) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 REFLECTION IN BIN (WORKING SET) : 989 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 39 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1722 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 173 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.80000 REMARK 3 B22 (A**2) : 0.80000 REMARK 3 B33 (A**2) : -1.21000 REMARK 3 B12 (A**2) : 0.40000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.152 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.110 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.050 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1809 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2455 ; 1.836 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 226 ; 7.772 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 93 ;36.222 ;23.548 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 309 ;15.789 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;18.583 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 259 ; 0.248 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1407 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1103 ; 0.930 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1780 ; 1.593 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 706 ; 2.823 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 670 ; 4.551 ; 4.500 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 : 16 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 12 A 21 REMARK 3 ORIGIN FOR THE GROUP (A): 20.5421 -33.0217 12.1677 REMARK 3 T TENSOR REMARK 3 T11: 0.2386 T22: 0.4970 REMARK 3 T33: 0.2382 T12: -0.0561 REMARK 3 T13: -0.0339 T23: 0.0333 REMARK 3 L TENSOR REMARK 3 L11: 5.2714 L22: 3.2599 REMARK 3 L33: 11.8446 L12: 3.1293 REMARK 3 L13: -4.6283 L23: -1.0520 REMARK 3 S TENSOR REMARK 3 S11: -0.1207 S12: -0.9599 S13: -0.3524 REMARK 3 S21: 0.1860 S22: 0.1923 S23: -0.2801 REMARK 3 S31: -0.0676 S32: 0.6391 S33: -0.0717 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 22 A 35 REMARK 3 ORIGIN FOR THE GROUP (A): 12.4608 -26.8944 1.8019 REMARK 3 T TENSOR REMARK 3 T11: 0.1529 T22: 0.1452 REMARK 3 T33: 0.1846 T12: -0.0260 REMARK 3 T13: 0.0524 T23: -0.0222 REMARK 3 L TENSOR REMARK 3 L11: 10.1877 L22: 2.3908 REMARK 3 L33: 10.2535 L12: 0.4140 REMARK 3 L13: 6.5379 L23: -0.9705 REMARK 3 S TENSOR REMARK 3 S11: -0.0523 S12: -0.3011 S13: 0.3270 REMARK 3 S21: 0.0876 S22: 0.0369 S23: 0.0984 REMARK 3 S31: -0.7248 S32: -0.3161 S33: 0.0153 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 36 A 41 REMARK 3 ORIGIN FOR THE GROUP (A): 3.6106 -27.7790 -10.3127 REMARK 3 T TENSOR REMARK 3 T11: 0.1844 T22: 0.2557 REMARK 3 T33: 0.1078 T12: -0.0222 REMARK 3 T13: 0.0196 T23: 0.1226 REMARK 3 L TENSOR REMARK 3 L11: 40.3432 L22: 7.0535 REMARK 3 L33: 8.5478 L12: 3.0367 REMARK 3 L13: -6.3945 L23: 1.8000 REMARK 3 S TENSOR REMARK 3 S11: -0.2143 S12: 1.3226 S13: 0.8720 REMARK 3 S21: -0.2686 S22: 0.2269 S23: 0.0097 REMARK 3 S31: -0.5567 S32: -0.1665 S33: -0.0126 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 42 A 59 REMARK 3 ORIGIN FOR THE GROUP (A): 14.3062 -33.1422 4.4504 REMARK 3 T TENSOR REMARK 3 T11: 0.1252 T22: 0.1999 REMARK 3 T33: 0.1326 T12: -0.0232 REMARK 3 T13: 0.0266 T23: -0.0450 REMARK 3 L TENSOR REMARK 3 L11: 7.3037 L22: 1.8419 REMARK 3 L33: 2.9963 L12: 0.8177 REMARK 3 L13: 3.0540 L23: 0.1221 REMARK 3 S TENSOR REMARK 3 S11: 0.0971 S12: -0.2666 S13: -0.3383 REMARK 3 S21: 0.1485 S22: 0.0216 S23: -0.1385 REMARK 3 S31: -0.0252 S32: -0.0334 S33: -0.1186 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 60 A 75 REMARK 3 ORIGIN FOR THE GROUP (A): 9.2076 -32.1009 0.8191 REMARK 3 T TENSOR REMARK 3 T11: 0.1168 T22: 0.1335 REMARK 3 T33: 0.0875 T12: -0.0088 REMARK 3 T13: 0.0481 T23: 0.0068 REMARK 3 L TENSOR REMARK 3 L11: 8.6084 L22: 1.1564 REMARK 3 L33: 2.7506 L12: -0.1005 REMARK 3 L13: 1.3547 L23: 0.2900 REMARK 3 S TENSOR REMARK 3 S11: 0.1141 S12: 0.0387 S13: 0.0153 REMARK 3 S21: 0.0964 S22: -0.0137 S23: 0.0554 REMARK 3 S31: -0.1933 S32: -0.0786 S33: -0.1004 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 76 A 89 REMARK 3 ORIGIN FOR THE GROUP (A): -4.3646 -29.1153 1.4505 REMARK 3 T TENSOR REMARK 3 T11: 0.1986 T22: 0.2504 REMARK 3 T33: 0.2143 T12: 0.0931 REMARK 3 T13: 0.0938 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 7.4205 L22: 4.2414 REMARK 3 L33: 14.1955 L12: 0.9339 REMARK 3 L13: -2.0173 L23: 2.1724 REMARK 3 S TENSOR REMARK 3 S11: 0.3132 S12: -0.2659 S13: 0.8359 REMARK 3 S21: 0.0078 S22: 0.1023 S23: 0.6291 REMARK 3 S31: -1.4176 S32: -0.1980 S33: -0.4156 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 90 A 99 REMARK 3 ORIGIN FOR THE GROUP (A): 4.0434 -38.9106 -2.3511 REMARK 3 T TENSOR REMARK 3 T11: 0.1478 T22: 0.1766 REMARK 3 T33: 0.1262 T12: 0.0167 REMARK 3 T13: -0.0032 T23: -0.0075 REMARK 3 L TENSOR REMARK 3 L11: 17.2098 L22: 2.1440 REMARK 3 L33: 2.4813 L12: 2.6243 REMARK 3 L13: 3.0273 L23: -0.6135 REMARK 3 S TENSOR REMARK 3 S11: 0.3435 S12: -0.3967 S13: -0.7738 REMARK 3 S21: 0.0060 S22: -0.0555 S23: -0.0570 REMARK 3 S31: 0.0930 S32: -0.1662 S33: -0.2879 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 : A 100 A 120 REMARK 3 ORIGIN FOR THE GROUP (A): 19.8188 -29.5714 -1.6696 REMARK 3 T TENSOR REMARK 3 T11: 0.1174 T22: 0.1881 REMARK 3 T33: 0.1109 T12: -0.0358 REMARK 3 T13: 0.0338 T23: -0.0255 REMARK 3 L TENSOR REMARK 3 L11: 7.4635 L22: 9.1323 REMARK 3 L33: 6.0007 L12: 6.3869 REMARK 3 L13: 5.3328 L23: 5.4067 REMARK 3 S TENSOR REMARK 3 S11: -0.2127 S12: 0.0922 S13: -0.1117 REMARK 3 S21: -0.2857 S22: 0.1570 S23: -0.0873 REMARK 3 S31: -0.2910 S32: 0.2489 S33: 0.0557 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 11 B 21 REMARK 3 ORIGIN FOR THE GROUP (A): -17.9772 -34.2606 4.0872 REMARK 3 T TENSOR REMARK 3 T11: 0.1366 T22: 0.4619 REMARK 3 T33: 0.2327 T12: 0.1241 REMARK 3 T13: -0.0420 T23: -0.0372 REMARK 3 L TENSOR REMARK 3 L11: 6.4810 L22: 8.0506 REMARK 3 L33: 13.8261 L12: 3.2241 REMARK 3 L13: -4.4646 L23: -2.1797 REMARK 3 S TENSOR REMARK 3 S11: -0.3694 S12: 1.2193 S13: -0.0337 REMARK 3 S21: -0.4184 S22: 0.7682 S23: 0.6336 REMARK 3 S31: 0.0659 S32: -0.7834 S33: -0.3989 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 22 B 40 REMARK 3 ORIGIN FOR THE GROUP (A): -8.2921 -27.5924 17.2043 REMARK 3 T TENSOR REMARK 3 T11: 0.1721 T22: 0.1739 REMARK 3 T33: 0.2043 T12: 0.0053 REMARK 3 T13: 0.0724 T23: -0.0167 REMARK 3 L TENSOR REMARK 3 L11: 14.1233 L22: 0.7118 REMARK 3 L33: 7.1491 L12: -1.5441 REMARK 3 L13: 6.5689 L23: 0.2625 REMARK 3 S TENSOR REMARK 3 S11: 0.0821 S12: -0.2918 S13: 0.5955 REMARK 3 S21: -0.0776 S22: 0.0433 S23: -0.1074 REMARK 3 S31: -0.6295 S32: 0.0133 S33: -0.1253 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 41 B 59 REMARK 3 ORIGIN FOR THE GROUP (A): -10.6309 -33.6372 12.3072 REMARK 3 T TENSOR REMARK 3 T11: 0.0931 T22: 0.2202 REMARK 3 T33: 0.1162 T12: 0.0414 REMARK 3 T13: 0.0273 T23: 0.0090 REMARK 3 L TENSOR REMARK 3 L11: 8.1989 L22: 1.5504 REMARK 3 L33: 2.3293 L12: -0.5361 REMARK 3 L13: 1.3418 L23: -0.3565 REMARK 3 S TENSOR REMARK 3 S11: 0.2562 S12: 0.3970 S13: -0.2204 REMARK 3 S21: -0.1446 S22: -0.0596 S23: 0.0168 REMARK 3 S31: -0.0519 S32: -0.0640 S33: -0.1966 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 60 B 74 REMARK 3 ORIGIN FOR THE GROUP (A): -7.1508 -33.2354 14.6260 REMARK 3 T TENSOR REMARK 3 T11: 0.1434 T22: 0.1822 REMARK 3 T33: 0.1231 T12: 0.0190 REMARK 3 T13: 0.0351 T23: -0.0129 REMARK 3 L TENSOR REMARK 3 L11: 7.4843 L22: 0.7727 REMARK 3 L33: 1.7894 L12: -0.1194 REMARK 3 L13: -0.1614 L23: -0.3559 REMARK 3 S TENSOR REMARK 3 S11: 0.1095 S12: 0.2089 S13: -0.1523 REMARK 3 S21: -0.0990 S22: 0.0238 S23: -0.0333 REMARK 3 S31: -0.3107 S32: -0.0838 S33: -0.1333 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 : B 75 B 82 REMARK 3 ORIGIN FOR THE GROUP (A): 3.3042 -21.9755 14.4291 REMARK 3 T TENSOR REMARK 3 T11: 0.7108 T22: 0.4872 REMARK 3 T33: 0.6026 T12: -0.2364 REMARK 3 T13: 0.0446 T23: -0.0837 REMARK 3 L TENSOR REMARK 3 L11: 9.3657 L22: -3.0890 REMARK 3 L33: 34.0550 L12: -3.1241 REMARK 3 L13: 9.5133 L23: -2.5981 REMARK 3 S TENSOR REMARK 3 S11: -0.1189 S12: 0.6316 S13: 0.2340 REMARK 3 S21: -0.0348 S22: -0.0562 S23: 0.0580 REMARK 3 S31: -1.3711 S32: 1.6222 S33: 0.1751 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 83 B 91 REMARK 3 ORIGIN FOR THE GROUP (A): 8.7800 -35.7762 16.2318 REMARK 3 T TENSOR REMARK 3 T11: 0.0847 T22: 0.2492 REMARK 3 T33: 0.2770 T12: -0.0423 REMARK 3 T13: -0.0084 T23: -0.0307 REMARK 3 L TENSOR REMARK 3 L11: 3.4460 L22: 5.7947 REMARK 3 L33: 13.4703 L12: 4.6729 REMARK 3 L13: -3.4890 L23: -4.7498 REMARK 3 S TENSOR REMARK 3 S11: 0.1149 S12: -0.0402 S13: -0.4076 REMARK 3 S21: 0.1194 S22: 0.0021 S23: -0.4950 REMARK 3 S31: 0.0548 S32: 0.5927 S33: -0.1170 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 : B 92 B 106 REMARK 3 ORIGIN FOR THE GROUP (A): -12.9515 -33.1387 15.9386 REMARK 3 T TENSOR REMARK 3 T11: 0.1516 T22: 0.2030 REMARK 3 T33: 0.1176 T12: 0.0048 REMARK 3 T13: 0.0129 T23: -0.0223 REMARK 3 L TENSOR REMARK 3 L11: 8.1299 L22: 3.6285 REMARK 3 L33: 2.2184 L12: -3.5686 REMARK 3 L13: 1.9950 L23: -1.1497 REMARK 3 S TENSOR REMARK 3 S11: -0.0343 S12: -0.2153 S13: -0.5696 REMARK 3 S21: 0.0372 S22: 0.1313 S23: 0.3436 REMARK 3 S31: -0.2311 S32: -0.1891 S33: -0.0970 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 107 B 120 REMARK 3 ORIGIN FOR THE GROUP (A): -14.2621 -32.5885 19.6654 REMARK 3 T TENSOR REMARK 3 T11: 0.1339 T22: 0.1899 REMARK 3 T33: 0.0828 T12: 0.0169 REMARK 3 T13: 0.0187 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 8.7324 L22: 9.7801 REMARK 3 L33: 3.9249 L12: -6.1009 REMARK 3 L13: 1.0040 L23: -1.4538 REMARK 3 S TENSOR REMARK 3 S11: -0.1800 S12: -0.1327 S13: -0.1664 REMARK 3 S21: 0.2980 S22: -0.0153 S23: 0.0012 REMARK 3 S31: -0.0797 S32: -0.2862 S33: 0.1953 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 REMARK 4 REMARK 4 3NX0 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-10. REMARK 100 THE RCSB ID CODE IS RCSB060384. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.81272 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20617 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.42900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE, 0.2 M REMARK 280 AMMONIUM SULFATE AND 25% PEG 8000, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 292K 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 32.57433 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 65.14867 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 48.86150 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 81.43583 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 16.28717 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 400 REMARK 400 COMPOUND REMARK 400 AUTHORS STATE THAT THE CHIRALITY CHANGE AT CA ATOM OF ASN A57 IS REMARK 400 CAUSED BY AN INTERMOLECULAR HYDROGEN BOND WITH H90 RESIDUE FROM A REMARK 400 MOLECULE RELATED BY CRYSTALLOGRAPHIC SYMMETRY. THIS INTERACTION REMARK 400 BETWEEN THE CARBONYL O ATOM OF N57 AND THE N ATOM OF H90 MAY REMARK 400 ADDITIONALLY FORCE THE ASPARAGINE TO ADOPT THE STRAINED REMARK 400 CONFORMATION. 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 SER A 1 REMARK 465 SER A 2 REMARK 465 PRO A 3 REMARK 465 GLY A 4 REMARK 465 LYS A 5 REMARK 465 PRO A 6 REMARK 465 PRO A 7 REMARK 465 ARG A 8 REMARK 465 LEU A 9 REMARK 465 VAL A 10 REMARK 465 GLY A 11 REMARK 465 SER B 1 REMARK 465 SER B 2 REMARK 465 PRO B 3 REMARK 465 GLY B 4 REMARK 465 LYS B 5 REMARK 465 PRO B 6 REMARK 465 PRO B 7 REMARK 465 ARG B 8 REMARK 465 LEU B 9 REMARK 465 VAL B 10 REMARK 465 GLY B 11 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 LEU A 47 CA - CB - CG ANGL. DEV. = 16.3 DEGREES REMARK 500 ASN A 57 N - CA - C ANGL. DEV. = 17.1 DEGREES REMARK 500 ASN B 57 N - CA - C ANGL. DEV. = 18.3 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 ASN A 57 -101.60 -142.73 REMARK 500 GLN A 77 119.21 -30.78 REMARK 500 ASN A 82 69.37 -153.48 REMARK 500 GLN B 48 125.35 -170.93 REMARK 500 ASN B 57 -99.11 -144.24 REMARK 500 PRO B 78 99.48 -45.46 REMARK 500 LEU B 80 -156.30 -148.84 REMARK 500 ASN B 82 32.52 -88.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASN A 57 -1.5 L D EXPECTING SP3 REMARK 500 ASN B 57 1.6 L L EXPECTING SP3 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 121 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 121 DBREF 3NX0 A 1 120 UNP P01034 CYTC_HUMAN 27 146 DBREF 3NX0 B 1 120 UNP P01034 CYTC_HUMAN 27 146 SEQADV 3NX0 ASN A 57 UNP P01034 VAL 83 ENGINEERED MUTATION SEQADV 3NX0 ASN B 57 UNP P01034 VAL 83 ENGINEERED MUTATION SEQRES 1 A 120 SER SER PRO GLY LYS PRO PRO ARG LEU VAL GLY GLY PRO SEQRES 2 A 120 MET ASP ALA SER VAL GLU GLU GLU GLY VAL ARG ARG ALA SEQRES 3 A 120 LEU ASP PHE ALA VAL GLY GLU TYR ASN LYS ALA SER ASN SEQRES 4 A 120 ASP MET TYR HIS SER ARG ALA LEU GLN VAL VAL ARG ALA SEQRES 5 A 120 ARG LYS GLN ILE ASN ALA GLY VAL ASN TYR PHE LEU ASP SEQRES 6 A 120 VAL GLU LEU GLY ARG THR THR CYS THR LYS THR GLN PRO SEQRES 7 A 120 ASN LEU ASP ASN CYS PRO PHE HIS ASP GLN PRO HIS LEU SEQRES 8 A 120 LYS ARG LYS ALA PHE CYS SER PHE GLN ILE TYR ALA VAL SEQRES 9 A 120 PRO TRP GLN GLY THR MET THR LEU SER LYS SER THR CYS SEQRES 10 A 120 GLN ASP ALA SEQRES 1 B 120 SER SER PRO GLY LYS PRO PRO ARG LEU VAL GLY GLY PRO SEQRES 2 B 120 MET ASP ALA SER VAL GLU GLU GLU GLY VAL ARG ARG ALA SEQRES 3 B 120 LEU ASP PHE ALA VAL GLY GLU TYR ASN LYS ALA SER ASN SEQRES 4 B 120 ASP MET TYR HIS SER ARG ALA LEU GLN VAL VAL ARG ALA SEQRES 5 B 120 ARG LYS GLN ILE ASN ALA GLY VAL ASN TYR PHE LEU ASP SEQRES 6 B 120 VAL GLU LEU GLY ARG THR THR CYS THR LYS THR GLN PRO SEQRES 7 B 120 ASN LEU ASP ASN CYS PRO PHE HIS ASP GLN PRO HIS LEU SEQRES 8 B 120 LYS ARG LYS ALA PHE CYS SER PHE GLN ILE TYR ALA VAL SEQRES 9 B 120 PRO TRP GLN GLY THR MET THR LEU SER LYS SER THR CYS SEQRES 10 B 120 GLN ASP ALA HET SO4 A 121 5 HET SO4 B 121 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *173(H2 O) HELIX 1 1 GLU A 20 SER A 38 1 19 HELIX 2 2 GLN A 88 ARG A 93 1 6 HELIX 3 3 PRO A 105 GLY A 108 5 4 HELIX 4 4 GLU B 20 SER B 38 1 19 HELIX 5 5 GLN B 88 ARG B 93 1 6 HELIX 6 6 PRO B 105 GLY B 108 5 4 SHEET 1 A 5 MET A 14 ASP A 15 0 SHEET 2 A 5 TYR A 42 ILE A 56 -1 O LYS A 54 N MET A 14 SHEET 3 A 5 VAL A 60 THR A 74 -1 O GLU A 67 N LEU A 47 SHEET 4 A 5 ALA A 95 VAL A 104 -1 O CYS A 97 N VAL A 66 SHEET 5 A 5 THR A 109 ASP A 119 -1 O GLN A 118 N PHE A 96 SHEET 1 B 5 MET B 14 ALA B 16 0 SHEET 2 B 5 TYR B 42 ILE B 56 -1 O LYS B 54 N MET B 14 SHEET 3 B 5 VAL B 60 THR B 74 -1 O GLU B 67 N LEU B 47 SHEET 4 B 5 ALA B 95 VAL B 104 -1 O CYS B 97 N VAL B 66 SHEET 5 B 5 THR B 109 ASP B 119 -1 O LYS B 114 N GLN B 100 SSBOND 1 CYS A 73 CYS A 83 1555 1555 2.05 SSBOND 2 CYS A 97 CYS A 117 1555 1555 2.08 SSBOND 3 CYS B 73 CYS B 83 1555 1555 2.04 SSBOND 4 CYS B 97 CYS B 117 1555 1555 2.09 CISPEP 1 GLY A 12 PRO A 13 0 3.43 CISPEP 2 GLY B 12 PRO B 13 0 7.17 SITE 1 AC1 6 ASN A 57 ALA A 58 GLY A 59 TYR A 102 SITE 2 AC1 6 HOH A 150 HOH A 181 SITE 1 AC2 6 ASN B 57 ALA B 58 GLY B 59 ASN B 61 SITE 2 AC2 6 TYR B 102 HOH B 190 CRYST1 76.316 76.316 97.723 90.00 90.00 120.00 P 61 12 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 0.013103 0.007565 0.000000 0.00000 SCALE2 0.000000 0.015131 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010233 0.00000