HEADER LIGASE 14-DEC-09 3L1Y TITLE CRYSTAL STRUCTURE OF HUMAN UBC4 E2 CONJUGATING ENZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-147; COMPND 5 SYNONYM: UBIQUITIN-PROTEIN LIGASE D2, UBIQUITIN CARRIER PROTEIN D2, COMPND 6 UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2, E2(17)KB 2; COMPND 7 EC: 6.3.2.19; COMPND 8 ENGINEERED: 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PT7.7 KEYWDS E2 CONJUGATING ENZYME, UBIQUITIN LIGASE, UBL CONJUGATION PATHWAY, KEYWDS 2 LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR R.BENIRSCHKE,J.R.THOMPSON,G.MER REVDAT 3 06-SEP-23 3L1Y 1 SEQADV REVDAT 2 25-AUG-10 3L1Y 1 JRNL REVDAT 1 05-MAY-10 3L1Y 0 JRNL AUTH R.C.BENIRSCHKE,J.R.THOMPSON,Y.NOMINE,E.WASIELEWSKI, JRNL AUTH 2 N.JURANIC,S.MACURA,S.HATAKEYAMA,K.I.NAKAYAMA,M.V.BOTUYAN, JRNL AUTH 3 G.MER JRNL TITL MOLECULAR BASIS FOR THE ASSOCIATION OF HUMAN E4B U BOX JRNL TITL 2 UBIQUITIN LIGASE WITH E2-CONJUGATING ENZYMES UBCH5C AND JRNL TITL 3 UBC4. JRNL REF STRUCTURE V. 18 955 2010 JRNL REFN ISSN 0969-2126 JRNL PMID 20696396 JRNL DOI 10.1016/J.STR.2010.04.017 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0063 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 17905 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 958 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1346 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4130 REMARK 3 BIN FREE R VALUE SET COUNT : 61 REMARK 3 BIN FREE R VALUE : 0.4570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1220 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 176 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 6.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : 0.13000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.21000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.105 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.236 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1320 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1813 ; 2.018 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 169 ; 6.263 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 64 ;32.328 ;23.594 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 217 ;12.409 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;18.879 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 192 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1050 ; 0.012 ; 0.022 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): 802 ; 0.970 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1321 ; 1.728 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 518 ; 3.287 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 485 ; 4.907 ; 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 : 5 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 0 A 6 REMARK 3 ORIGIN FOR THE GROUP (A): 0.8050 3.9460 35.4670 REMARK 3 T TENSOR REMARK 3 T11: 0.1262 T22: 0.2698 REMARK 3 T33: 0.0616 T12: -0.0042 REMARK 3 T13: 0.0055 T23: 0.0343 REMARK 3 L TENSOR REMARK 3 L11: 0.5594 L22: 4.3879 REMARK 3 L33: 16.0278 L12: -1.5142 REMARK 3 L13: 0.6397 L23: 0.3564 REMARK 3 S TENSOR REMARK 3 S11: -0.0775 S12: 0.0802 S13: -0.0321 REMARK 3 S21: 0.2467 S22: -0.1384 S23: 0.1119 REMARK 3 S31: 0.3516 S32: 0.8198 S33: 0.2159 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 7 A 21 REMARK 3 ORIGIN FOR THE GROUP (A): -1.8050 -3.4230 18.4300 REMARK 3 T TENSOR REMARK 3 T11: 0.1868 T22: 0.1331 REMARK 3 T33: 0.0616 T12: 0.0102 REMARK 3 T13: -0.0086 T23: 0.0206 REMARK 3 L TENSOR REMARK 3 L11: 0.8032 L22: 3.5877 REMARK 3 L33: 5.6672 L12: -0.4773 REMARK 3 L13: -0.9276 L23: 3.1381 REMARK 3 S TENSOR REMARK 3 S11: -0.1050 S12: -0.1390 S13: -0.1850 REMARK 3 S21: 0.1211 S22: 0.0017 S23: 0.0361 REMARK 3 S31: 0.2551 S32: 0.0413 S33: 0.1033 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 22 A 92 REMARK 3 ORIGIN FOR THE GROUP (A): 1.6270 8.7570 8.1630 REMARK 3 T TENSOR REMARK 3 T11: 0.1861 T22: 0.1142 REMARK 3 T33: 0.0409 T12: -0.0105 REMARK 3 T13: -0.0214 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 0.1733 L22: 0.7938 REMARK 3 L33: 2.4903 L12: 0.1758 REMARK 3 L13: -0.4176 L23: -1.0589 REMARK 3 S TENSOR REMARK 3 S11: 0.0239 S12: -0.0239 S13: 0.0341 REMARK 3 S21: -0.0979 S22: 0.0510 S23: 0.0412 REMARK 3 S31: 0.0379 S32: -0.0078 S33: -0.0748 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 93 A 117 REMARK 3 ORIGIN FOR THE GROUP (A): -8.1570 8.7790 9.6410 REMARK 3 T TENSOR REMARK 3 T11: 0.1760 T22: 0.1511 REMARK 3 T33: 0.0903 T12: -0.0025 REMARK 3 T13: -0.0276 T23: 0.0322 REMARK 3 L TENSOR REMARK 3 L11: 1.1766 L22: 1.3790 REMARK 3 L33: 4.2122 L12: 0.6613 REMARK 3 L13: -0.6527 L23: -1.2629 REMARK 3 S TENSOR REMARK 3 S11: -0.0290 S12: 0.1478 S13: 0.1400 REMARK 3 S21: -0.0953 S22: 0.1959 S23: 0.2218 REMARK 3 S31: -0.0627 S32: -0.3079 S33: -0.1670 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 118 A 151 REMARK 3 ORIGIN FOR THE GROUP (A): -2.5380 16.1620 -9.1630 REMARK 3 T TENSOR REMARK 3 T11: 0.1979 T22: 0.1006 REMARK 3 T33: 0.0237 T12: -0.0278 REMARK 3 T13: -0.0204 T23: 0.0078 REMARK 3 L TENSOR REMARK 3 L11: 1.9869 L22: 2.9662 REMARK 3 L33: 2.5686 L12: -1.4800 REMARK 3 L13: 0.8962 L23: -0.7565 REMARK 3 S TENSOR REMARK 3 S11: 0.0069 S12: 0.0196 S13: -0.0251 REMARK 3 S21: -0.1111 S22: -0.0106 S23: 0.1169 REMARK 3 S31: 0.0004 S32: -0.1505 S33: 0.0037 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 3L1Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000056730. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17905 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 43.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.1400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.12300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 13.15 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 1X23 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M SODIUM FORMATE, 0.1M SODIUM ACETATE REMARK 280 TRIHYDRATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295K 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 29.56000 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 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 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 MET A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP A 29 O HOH A 224 1.97 REMARK 500 O HOH A 174 O HOH A 267 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1 ASN A -1 O HOH A 290 1656 2.19 REMARK 500 REMARK 500 REMARK: NULL 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. = -3.4 DEGREES REMARK 500 ASP A 59 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 TYR A 134 CB - CG - CD1 ANGL. DEV. = -4.2 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 42 64.40 -105.01 REMARK 500 ARG A 90 -116.18 -134.06 REMARK 500 ASN A 114 76.80 -109.94 REMARK 500 ASP A 130 80.43 -156.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3L1X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF U-BOX DOMAIN OF HUMAN E4B UBIQUITIN LIGASE REMARK 900 RELATED ID: 3L1Z RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE U-BOX DOMAIN OF HUMAN E4B UBIQUITIN LIGASE REMARK 900 IN COMPLEX WITH UBCH5C E2 UBIQUITIN CONJUGATING ENZYME REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE RESIDUE AT POSITION 128 IS A NATURAL VARIANT AS IN AAC41750 DBREF 3L1Y A 1 147 UNP P62837 UB2D2_HUMAN 1 147 SEQADV 3L1Y MET A -9 UNP P62837 EXPRESSION TAG SEQADV 3L1Y HIS A -8 UNP P62837 EXPRESSION TAG SEQADV 3L1Y HIS A -7 UNP P62837 EXPRESSION TAG SEQADV 3L1Y HIS A -6 UNP P62837 EXPRESSION TAG SEQADV 3L1Y HIS A -5 UNP P62837 EXPRESSION TAG SEQADV 3L1Y HIS A -4 UNP P62837 EXPRESSION TAG SEQADV 3L1Y HIS A -3 UNP P62837 EXPRESSION TAG SEQADV 3L1Y MET A -2 UNP P62837 EXPRESSION TAG SEQADV 3L1Y ASN A -1 UNP P62837 EXPRESSION TAG SEQADV 3L1Y SER A 0 UNP P62837 EXPRESSION TAG SEQADV 3L1Y GLN A 128 UNP P62837 LYS 128 SEE REMARK 999 SEQRES 1 A 157 MET HIS HIS HIS HIS HIS HIS MET ASN SER MET ALA LEU SEQRES 2 A 157 LYS ARG ILE HIS LYS GLU LEU ASN ASP LEU ALA ARG ASP SEQRES 3 A 157 PRO PRO ALA GLN CYS SER ALA GLY PRO VAL GLY ASP ASP SEQRES 4 A 157 MET PHE HIS TRP GLN ALA THR ILE MET GLY PRO ASN ASP SEQRES 5 A 157 SER PRO TYR GLN GLY GLY VAL PHE PHE LEU THR ILE HIS SEQRES 6 A 157 PHE PRO THR ASP TYR PRO PHE LYS PRO PRO LYS VAL ALA SEQRES 7 A 157 PHE THR THR ARG ILE TYR HIS PRO ASN ILE ASN SER ASN SEQRES 8 A 157 GLY SER ILE CYS LEU ASP ILE LEU ARG SER GLN TRP SER SEQRES 9 A 157 PRO ALA LEU THR ILE SER LYS VAL LEU LEU SER ILE CYS SEQRES 10 A 157 SER LEU LEU CYS ASP PRO ASN PRO ASP ASP PRO LEU VAL SEQRES 11 A 157 PRO GLU ILE ALA ARG ILE TYR GLN THR ASP ARG GLU LYS SEQRES 12 A 157 TYR ASN ARG ILE ALA ARG GLU TRP THR GLN LYS TYR ALA SEQRES 13 A 157 MET FORMUL 2 HOH *176(H2 O) HELIX 1 1 SER A 0 ASP A 16 1 17 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 THR A 36 N SER A 22 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 11.59 CRYST1 28.230 59.120 45.240 90.00 106.73 90.00 P 1 21 1 2 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 0.035423 0.000000 0.010648 0.00000 SCALE2 0.000000 0.016915 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023081 0.00000