PDB Short entry for 2ESP HEADER LIGASE 26-OCT-05 2ESP TITLE HUMAN UBIQUITIN-CONJUGATING ENZYME (E2) UBCH5B MUTANT ILE88ALA COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBIQUITIN-PROTEIN LIGASE D2, UBIQUITIN CARRIER PROTEIN D2, COMPND 5 UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2, E217, KB 2; COMPND 6 EC: 6.3.2.19; 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: UBE2D2, UBC4, UBCH5B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHIS-PARALLEL KEYWDS LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR E.OZKAN,H.YU,J.DEISENHOFER REVDAT 7 23-AUG-23 2ESP 1 REMARK REVDAT 6 20-OCT-21 2ESP 1 REMARK SEQADV REVDAT 5 18-OCT-17 2ESP 1 REMARK REVDAT 4 13-JUL-11 2ESP 1 VERSN REVDAT 3 24-FEB-09 2ESP 1 VERSN REVDAT 2 10-JAN-06 2ESP 1 JRNL REVDAT 1 06-DEC-05 2ESP 0 JRNL AUTH E.OZKAN,H.YU,J.DEISENHOFER JRNL TITL MECHANISTIC INSIGHT INTO THE ALLOSTERIC ACTIVATION OF A JRNL TITL 2 UBIQUITIN-CONJUGATING ENZYME BY RING-TYPE UBIQUITIN LIGASES JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 18890 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 16365295 JRNL DOI 10.1073/PNAS.0509418102 REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REFMAC_5.2.0005 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) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 21765 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1168 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) : 1.52 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1405 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1184 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 136 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.18000 REMARK 3 B22 (A**2) : -0.35000 REMARK 3 B33 (A**2) : 0.53000 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): 0.082 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.091 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.056 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.950 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1261 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1731 ; 2.084 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 160 ;13.488 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 55 ;32.036 ;23.455 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 201 ;13.101 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;17.492 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 188 ; 0.138 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 982 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 606 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 887 ; 0.326 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 102 ; 0.159 ; 0.200 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): 52 ; 0.169 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.139 ; 0.200 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): 795 ; 1.182 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1270 ; 1.595 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 533 ; 2.662 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 456 ; 4.035 ; 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -1 A 5 REMARK 3 ORIGIN FOR THE GROUP (A): 37.7540 -6.8970 58.8130 REMARK 3 T TENSOR REMARK 3 T11: -0.0492 T22: -0.0149 REMARK 3 T33: 0.0018 T12: 0.0226 REMARK 3 T13: 0.0017 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 14.1283 L22: 4.6031 REMARK 3 L33: 4.3376 L12: 4.9742 REMARK 3 L13: 2.1334 L23: 1.6853 REMARK 3 S TENSOR REMARK 3 S11: 0.0863 S12: 0.0567 S13: 0.0605 REMARK 3 S21: -0.0117 S22: 0.0214 S23: -0.3217 REMARK 3 S31: 0.0646 S32: 0.2310 S33: -0.1078 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 6 A 10 REMARK 3 ORIGIN FOR THE GROUP (A): 31.4410 -4.9270 54.9730 REMARK 3 T TENSOR REMARK 3 T11: -0.0394 T22: -0.0337 REMARK 3 T33: -0.0333 T12: 0.0065 REMARK 3 T13: 0.0067 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 6.8662 L22: 6.8554 REMARK 3 L33: 1.7220 L12: 0.6788 REMARK 3 L13: 1.4521 L23: -1.4315 REMARK 3 S TENSOR REMARK 3 S11: 0.1323 S12: 0.0270 S13: 0.1769 REMARK 3 S21: -0.1835 S22: -0.0441 S23: -0.0416 REMARK 3 S31: 0.0824 S32: 0.0461 S33: -0.0882 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 11 A 17 REMARK 3 ORIGIN FOR THE GROUP (A): 24.2960 -6.9500 49.5670 REMARK 3 T TENSOR REMARK 3 T11: 0.0204 T22: 0.0027 REMARK 3 T33: 0.0299 T12: 0.0149 REMARK 3 T13: -0.0356 T23: -0.0331 REMARK 3 L TENSOR REMARK 3 L11: 15.3181 L22: 14.0194 REMARK 3 L33: 5.7878 L12: -4.8643 REMARK 3 L13: 4.9613 L23: -0.0018 REMARK 3 S TENSOR REMARK 3 S11: 0.1331 S12: 0.5333 S13: -0.5185 REMARK 3 S21: -0.3550 S22: -0.1915 S23: 0.6991 REMARK 3 S31: 0.0105 S32: 0.2098 S33: 0.0584 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 18 A 23 REMARK 3 ORIGIN FOR THE GROUP (A): 16.1160 -2.8190 54.6420 REMARK 3 T TENSOR REMARK 3 T11: 0.0104 T22: 0.1122 REMARK 3 T33: -0.0665 T12: -0.0615 REMARK 3 T13: -0.0106 T23: -0.0326 REMARK 3 L TENSOR REMARK 3 L11: 43.3612 L22: 16.4181 REMARK 3 L33: 6.9745 L12: 9.6947 REMARK 3 L13: -9.1130 L23: 2.3942 REMARK 3 S TENSOR REMARK 3 S11: -0.9403 S12: 1.4006 S13: -0.5279 REMARK 3 S21: -0.4713 S22: 0.3195 S23: 0.5786 REMARK 3 S31: 0.3558 S32: -0.6293 S33: 0.6208 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 24 A 29 REMARK 3 ORIGIN FOR THE GROUP (A): 30.6340 6.4450 57.2030 REMARK 3 T TENSOR REMARK 3 T11: 0.0006 T22: -0.0276 REMARK 3 T33: 0.0409 T12: 0.0062 REMARK 3 T13: 0.0252 T23: -0.0095 REMARK 3 L TENSOR REMARK 3 L11: 5.7157 L22: 11.0855 REMARK 3 L33: 7.7389 L12: 5.8708 REMARK 3 L13: 1.1299 L23: -2.5545 REMARK 3 S TENSOR REMARK 3 S11: -0.1646 S12: 0.4569 S13: 0.3079 REMARK 3 S21: -0.0364 S22: 0.1950 S23: -0.4122 REMARK 3 S31: -0.4368 S32: 0.0120 S33: -0.0304 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 30 A 33 REMARK 3 ORIGIN FOR THE GROUP (A): 30.9530 2.2010 60.5910 REMARK 3 T TENSOR REMARK 3 T11: -0.0499 T22: -0.0311 REMARK 3 T33: -0.0176 T12: -0.0024 REMARK 3 T13: -0.0011 T23: -0.0148 REMARK 3 L TENSOR REMARK 3 L11: 12.6755 L22: 2.9524 REMARK 3 L33: 2.2285 L12: -2.7290 REMARK 3 L13: 2.1104 L23: -0.9649 REMARK 3 S TENSOR REMARK 3 S11: -0.0236 S12: -0.1541 S13: 0.2214 REMARK 3 S21: 0.1017 S22: 0.0619 S23: -0.3725 REMARK 3 S31: 0.0964 S32: 0.0534 S33: -0.0383 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 34 A 43 REMARK 3 ORIGIN FOR THE GROUP (A): 10.5360 -0.6710 59.1930 REMARK 3 T TENSOR REMARK 3 T11: -0.0403 T22: -0.0171 REMARK 3 T33: -0.0385 T12: -0.0045 REMARK 3 T13: -0.0233 T23: 0.0124 REMARK 3 L TENSOR REMARK 3 L11: 33.0002 L22: 5.8973 REMARK 3 L33: 0.8715 L12: 12.3706 REMARK 3 L13: 0.7986 L23: 0.9506 REMARK 3 S TENSOR REMARK 3 S11: -0.3391 S12: 0.7153 S13: 0.0539 REMARK 3 S21: -0.1826 S22: 0.3170 S23: 0.0572 REMARK 3 S31: 0.0039 S32: 0.0887 S33: 0.0221 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 44 A 51 REMARK 3 ORIGIN FOR THE GROUP (A): 8.1860 2.7540 61.9210 REMARK 3 T TENSOR REMARK 3 T11: -0.0476 T22: -0.0187 REMARK 3 T33: -0.0446 T12: 0.0124 REMARK 3 T13: -0.0098 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 4.9409 L22: 5.4115 REMARK 3 L33: 1.1891 L12: 0.9879 REMARK 3 L13: 0.7303 L23: -0.7365 REMARK 3 S TENSOR REMARK 3 S11: 0.0523 S12: 0.2964 S13: 0.2514 REMARK 3 S21: -0.0582 S22: 0.0665 S23: 0.1987 REMARK 3 S31: -0.0061 S32: 0.1245 S33: -0.1188 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 52 A 61 REMARK 3 ORIGIN FOR THE GROUP (A): 30.4790 -2.2800 65.3520 REMARK 3 T TENSOR REMARK 3 T11: -0.0427 T22: -0.0033 REMARK 3 T33: -0.0271 T12: 0.0005 REMARK 3 T13: -0.0242 T23: -0.0095 REMARK 3 L TENSOR REMARK 3 L11: 3.3101 L22: 3.3682 REMARK 3 L33: 0.3267 L12: -2.0873 REMARK 3 L13: -1.0303 L23: 0.7605 REMARK 3 S TENSOR REMARK 3 S11: -0.0144 S12: -0.0041 S13: 0.0890 REMARK 3 S21: 0.0674 S22: 0.0309 S23: -0.1372 REMARK 3 S31: 0.0385 S32: 0.0209 S33: -0.0164 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 : A 62 A 68 REMARK 3 ORIGIN FOR THE GROUP (A): 29.2040 -5.2660 68.8810 REMARK 3 T TENSOR REMARK 3 T11: -0.0179 T22: 0.0077 REMARK 3 T33: -0.0587 T12: 0.0155 REMARK 3 T13: 0.0017 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 33.8551 L22: 30.6176 REMARK 3 L33: 1.5964 L12: -30.5967 REMARK 3 L13: 1.6386 L23: -0.6381 REMARK 3 S TENSOR REMARK 3 S11: -0.2872 S12: -0.0406 S13: 0.2218 REMARK 3 S21: 0.5437 S22: 0.2030 S23: -0.1709 REMARK 3 S31: 0.1129 S32: 0.0052 S33: 0.0842 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 69 A 73 REMARK 3 ORIGIN FOR THE GROUP (A): 13.3670 5.7530 68.5890 REMARK 3 T TENSOR REMARK 3 T11: 0.0446 T22: 0.0470 REMARK 3 T33: 0.0679 T12: 0.0183 REMARK 3 T13: -0.0565 T23: -0.0911 REMARK 3 L TENSOR REMARK 3 L11: 14.9531 L22: 3.7635 REMARK 3 L33: 5.7055 L12: -1.3578 REMARK 3 L13: -4.5641 L23: -3.5476 REMARK 3 S TENSOR REMARK 3 S11: -0.2206 S12: -0.4491 S13: 0.6259 REMARK 3 S21: 0.1187 S22: 0.2949 S23: -0.2016 REMARK 3 S31: -0.1738 S32: 0.2765 S33: -0.0743 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 : A 74 A 79 REMARK 3 ORIGIN FOR THE GROUP (A): 9.9580 -0.5850 73.8710 REMARK 3 T TENSOR REMARK 3 T11: -0.0060 T22: -0.0075 REMARK 3 T33: -0.0744 T12: 0.0154 REMARK 3 T13: 0.0076 T23: -0.0066 REMARK 3 L TENSOR REMARK 3 L11: 2.2306 L22: 4.9405 REMARK 3 L33: 4.8590 L12: -0.3699 REMARK 3 L13: -1.9650 L23: 0.0738 REMARK 3 S TENSOR REMARK 3 S11: 0.0164 S12: -0.0984 S13: -0.1136 REMARK 3 S21: 0.0723 S22: 0.0089 S23: -0.0130 REMARK 3 S31: -0.1526 S32: 0.0402 S33: -0.0253 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 80 A 89 REMARK 3 ORIGIN FOR THE GROUP (A): 18.8840 -3.1610 73.1750 REMARK 3 T TENSOR REMARK 3 T11: 0.0134 T22: 0.0824 REMARK 3 T33: -0.0400 T12: -0.0027 REMARK 3 T13: -0.0345 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 9.9836 L22: 22.5794 REMARK 3 L33: 4.9421 L12: -10.6437 REMARK 3 L13: -5.4128 L23: 4.7782 REMARK 3 S TENSOR REMARK 3 S11: -0.3036 S12: -0.1340 S13: -0.0679 REMARK 3 S21: 0.2819 S22: 0.0028 S23: -0.2294 REMARK 3 S31: 0.0975 S32: 0.0666 S33: 0.3007 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 : A 90 A 97 REMARK 3 ORIGIN FOR THE GROUP (A): 26.2850 -12.6570 69.3640 REMARK 3 T TENSOR REMARK 3 T11: 0.0584 T22: 0.0347 REMARK 3 T33: -0.0246 T12: 0.0015 REMARK 3 T13: 0.0358 T23: 0.0131 REMARK 3 L TENSOR REMARK 3 L11: 8.8716 L22: 13.6950 REMARK 3 L33: 15.0843 L12: -4.3060 REMARK 3 L13: -1.2415 L23: 5.7102 REMARK 3 S TENSOR REMARK 3 S11: -0.1986 S12: -0.7768 S13: -0.1879 REMARK 3 S21: 1.1100 S22: 0.1563 S23: 0.2574 REMARK 3 S31: 0.1543 S32: -0.1595 S33: 0.0423 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 98 A 110 REMARK 3 ORIGIN FOR THE GROUP (A): 17.4100 -7.6960 62.8980 REMARK 3 T TENSOR REMARK 3 T11: -0.0380 T22: -0.0517 REMARK 3 T33: -0.0556 T12: -0.0009 REMARK 3 T13: -0.0007 T23: -0.0064 REMARK 3 L TENSOR REMARK 3 L11: 10.8357 L22: 0.8600 REMARK 3 L33: 1.7630 L12: -0.3038 REMARK 3 L13: -2.9381 L23: 0.3350 REMARK 3 S TENSOR REMARK 3 S11: -0.0658 S12: 0.0254 S13: 0.0103 REMARK 3 S21: 0.0671 S22: 0.0418 S23: -0.0492 REMARK 3 S31: 0.0100 S32: -0.0706 S33: 0.0240 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 : A 111 A 118 REMARK 3 ORIGIN FOR THE GROUP (A): 9.7820 -9.5500 74.9030 REMARK 3 T TENSOR REMARK 3 T11: 0.1557 T22: 0.0504 REMARK 3 T33: 0.0120 T12: -0.0296 REMARK 3 T13: 0.0430 T23: -0.0191 REMARK 3 L TENSOR REMARK 3 L11: 5.6318 L22: 10.3778 REMARK 3 L33: 30.5808 L12: 3.5289 REMARK 3 L13: 0.8176 L23: -1.5912 REMARK 3 S TENSOR REMARK 3 S11: 0.3062 S12: -0.4671 S13: -0.0399 REMARK 3 S21: 1.2751 S22: -0.5682 S23: 0.1388 REMARK 3 S31: 0.6709 S32: 0.9110 S33: 0.2620 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 119 A 131 REMARK 3 ORIGIN FOR THE GROUP (A): 2.8780 -3.8030 78.5290 REMARK 3 T TENSOR REMARK 3 T11: 0.0235 T22: -0.0038 REMARK 3 T33: -0.0413 T12: -0.0026 REMARK 3 T13: 0.0487 T23: -0.0206 REMARK 3 L TENSOR REMARK 3 L11: 4.6801 L22: 2.9156 REMARK 3 L33: 4.4848 L12: 1.8117 REMARK 3 L13: 1.3613 L23: 1.5354 REMARK 3 S TENSOR REMARK 3 S11: -0.0078 S12: -0.0978 S13: -0.1755 REMARK 3 S21: 0.2690 S22: -0.1057 S23: 0.0712 REMARK 3 S31: 0.2984 S32: 0.0273 S33: 0.1134 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 : A 132 A 136 REMARK 3 ORIGIN FOR THE GROUP (A): -2.8470 -0.5010 71.8690 REMARK 3 T TENSOR REMARK 3 T11: 0.0115 T22: -0.0178 REMARK 3 T33: 0.0472 T12: 0.0054 REMARK 3 T13: 0.0578 T23: -0.0517 REMARK 3 L TENSOR REMARK 3 L11: 9.5535 L22: 6.0041 REMARK 3 L33: 11.4446 L12: -3.2654 REMARK 3 L13: 3.2630 L23: -5.1756 REMARK 3 S TENSOR REMARK 3 S11: 0.0248 S12: -0.1440 S13: 0.1292 REMARK 3 S21: 0.1548 S22: -0.0031 S23: 0.3352 REMARK 3 S31: -0.1544 S32: -0.4114 S33: -0.0217 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 137 A 141 REMARK 3 ORIGIN FOR THE GROUP (A): 0.9990 5.1090 69.6010 REMARK 3 T TENSOR REMARK 3 T11: -0.0345 T22: -0.0200 REMARK 3 T33: 0.0279 T12: 0.0243 REMARK 3 T13: 0.0261 T23: -0.0137 REMARK 3 L TENSOR REMARK 3 L11: 2.5607 L22: 12.9611 REMARK 3 L33: 13.7799 L12: -0.4559 REMARK 3 L13: -0.0148 L23: 3.9747 REMARK 3 S TENSOR REMARK 3 S11: 0.0615 S12: -0.1673 S13: -0.0171 REMARK 3 S21: 0.6173 S22: -0.1860 S23: 0.4587 REMARK 3 S31: -0.0909 S32: -0.4773 S33: 0.1245 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 : A 142 A 147 REMARK 3 ORIGIN FOR THE GROUP (A): 5.2180 9.5280 64.7290 REMARK 3 T TENSOR REMARK 3 T11: -0.0236 T22: -0.0249 REMARK 3 T33: 0.0165 T12: 0.0233 REMARK 3 T13: -0.0160 T23: 0.0119 REMARK 3 L TENSOR REMARK 3 L11: 2.4544 L22: 9.9936 REMARK 3 L33: 5.4866 L12: 2.1422 REMARK 3 L13: -1.3830 L23: 2.0789 REMARK 3 S TENSOR REMARK 3 S11: 0.0605 S12: 0.0516 S13: 0.2111 REMARK 3 S21: -0.0030 S22: 0.0342 S23: 0.2439 REMARK 3 S31: -0.1385 S32: -0.2330 S33: -0.0947 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 : 1.20 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 2ESP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1000035045. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.97897 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22996 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.52200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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: PDB ENTRY 2ESK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NACL, PEG 6000, SODIUM ACETATE, REMARK 280 TEMPERATURE 294K, PH 4.5, VAPOR DIFFUSION, HANGING DROP 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 23.93850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.06400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.61200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.06400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.93850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.61200 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 ARG A 5 NE - CZ - NH2 ANGL. DEV. = 5.3 DEGREES REMARK 500 GLY A 27 C - N - CA ANGL. DEV. = 13.6 DEGREES REMARK 500 ARG A 125 CG - CD - NE ANGL. DEV. = -13.7 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 PRO A 18 -173.74 -53.78 REMARK 500 GLN A 20 5.78 81.46 REMARK 500 ARG A 90 -116.63 -135.53 REMARK 500 PRO A 113 160.84 -49.92 REMARK 500 ASP A 117 66.51 -117.10 REMARK 500 ASP A 130 81.85 -150.40 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 CL A 148 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 151 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ESK RELATED DB: PDB REMARK 900 RELATED ID: 2ESO RELATED DB: PDB REMARK 900 RELATED ID: 2ESQ RELATED DB: PDB DBREF 2ESP A 1 147 UNP P62837 UB2D2_HUMAN 1 147 SEQADV 2ESP GLY A -1 UNP P62837 CLONING ARTIFACT SEQADV 2ESP ALA A 0 UNP P62837 CLONING ARTIFACT SEQADV 2ESP ALA A 88 UNP P62837 ILE 88 ENGINEERED MUTATION SEQRES 1 A 149 GLY ALA MET ALA LEU LYS ARG ILE HIS LYS GLU LEU ASN SEQRES 2 A 149 ASP LEU ALA ARG ASP PRO PRO ALA GLN CYS SER ALA GLY SEQRES 3 A 149 PRO VAL GLY ASP ASP MET PHE HIS TRP GLN ALA THR ILE SEQRES 4 A 149 MET GLY PRO ASN ASP SER PRO TYR GLN GLY GLY VAL PHE SEQRES 5 A 149 PHE LEU THR ILE HIS PHE PRO THR ASP TYR PRO PHE LYS SEQRES 6 A 149 PRO PRO LYS VAL ALA PHE THR THR ARG ILE TYR HIS PRO SEQRES 7 A 149 ASN ILE ASN SER ASN GLY SER ILE CYS LEU ASP ALA LEU SEQRES 8 A 149 ARG SER GLN TRP SER PRO ALA LEU THR ILE SER LYS VAL SEQRES 9 A 149 LEU LEU SER ILE CYS SER LEU LEU CYS ASP PRO ASN PRO SEQRES 10 A 149 ASP ASP PRO LEU VAL PRO GLU ILE ALA ARG ILE TYR LYS SEQRES 11 A 149 THR ASP ARG GLU LYS TYR ASN ARG ILE ALA ARG GLU TRP SEQRES 12 A 149 THR GLN LYS TYR ALA MET HET CL A 148 1 HET MPD A 151 8 HETNAM CL CHLORIDE ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 CL CL 1- FORMUL 3 MPD C6 H14 O2 FORMUL 4 HOH *136(H2 O) HELIX 1 1 GLY A -1 ASP A 16 1 18 HELIX 2 2 LEU A 86 ARG A 90 5 5 HELIX 3 3 THR A 98 ASP A 112 1 15 HELIX 4 4 VAL A 120 ASP A 130 1 11 HELIX 5 5 ASP A 130 ALA A 146 1 17 SHEET 1 A 4 CYS A 21 PRO A 25 0 SHEET 2 A 4 HIS A 32 MET A 38 -1 O GLN A 34 N GLY A 24 SHEET 3 A 4 VAL A 49 HIS A 55 -1 O ILE A 54 N TRP A 33 SHEET 4 A 4 LYS A 66 PHE A 69 -1 O LYS A 66 N HIS A 55 CISPEP 1 TYR A 60 PRO A 61 0 5.41 SITE 1 AC1 3 MET A 1 LYS A 8 SER A 108 SITE 1 AC2 8 LYS A 4 ALA A 88 LEU A 97 LYS A 101 SITE 2 AC2 8 SER A 105 HOH A 154 HOH A 194 HOH A 228 CRYST1 47.877 49.224 62.128 90.00 90.00 90.00 P 21 21 21 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 0.020887 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020315 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016096 0.00000