HEADER TRANSFERASE 01-MAY-17 5VNZ TITLE STRUCTURE OF A TRAF6-UBC13~UB COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TNF RECEPTOR-ASSOCIATED FACTOR 6; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: RESIDUES 50-159; COMPND 5 SYNONYM: E3 UBIQUITIN-PROTEIN LIGASE TRAF6,RING-TYPE E3 UBIQUITIN COMPND 6 TRANSFERASE TRAF6; COMPND 7 EC: 2.3.2.27; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 N; COMPND 11 CHAIN: B, E; COMPND 12 SYNONYM: BENDLESS-LIKE UBIQUITIN-CONJUGATING ENZYME,E2 UBIQUITIN- COMPND 13 CONJUGATING ENZYME N,UBC13,UBCH13,UBIQUITIN CARRIER PROTEIN N, COMPND 14 UBIQUITIN-PROTEIN LIGASE N; COMPND 15 EC: 2.3.2.23; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 3; COMPND 18 MOLECULE: UBIQUITIN; COMPND 19 CHAIN: C, F; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: TRAF6, SI:DKEY-56P7.3, ZGC:63704; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: UBE2N, BLU; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: UBB; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.J.MIDDLETON,C.L.DAY REVDAT 2 04-OCT-23 5VNZ 1 REMARK REVDAT 1 06-DEC-17 5VNZ 0 JRNL AUTH A.J.MIDDLETON,R.BUDHIDARMO,A.DAS,J.ZHU,M.FOGLIZZO,P.D.MACE, JRNL AUTH 2 C.L.DAY JRNL TITL THE ACTIVITY OF TRAF RING HOMO- AND HETERODIMERS IS JRNL TITL 2 REGULATED BY ZINC FINGER 1. JRNL REF NAT COMMUN V. 8 1788 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 29176576 JRNL DOI 10.1038/S41467-017-01665-3 REMARK 2 REMARK 2 RESOLUTION. 3.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 107.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 15243 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) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 788 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) : 3.41 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.50 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1066 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.08 REMARK 3 BIN R VALUE (WORKING SET) : 0.4100 REMARK 3 BIN FREE R VALUE SET COUNT : 56 REMARK 3 BIN FREE R VALUE : 0.3820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5321 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 155.8 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.08000 REMARK 3 B22 (A**2) : 1.58000 REMARK 3 B33 (A**2) : -8.66000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.604 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.505 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 34.845 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.881 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5449 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5140 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7365 ; 1.086 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11969 ; 0.859 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 662 ; 5.930 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 256 ;36.030 ;24.609 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 993 ;14.032 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;13.067 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 818 ; 0.062 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5936 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1026 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 3 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 53 159 D 53 159 6170 0.060 0.050 REMARK 3 2 B 3 149 E 3 149 8774 0.070 0.050 REMARK 3 3 C 1 76 F 1 76 4380 0.040 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5VNZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000227443. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16046 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.410 REMARK 200 RESOLUTION RANGE LOW (A) : 107.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 1.54500 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: PHASER REMARK 200 STARTING MODEL: 3HCT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05-0.3 MM SODIUM CITRATE, 100 MM REMARK 280 BBIS-TRIS PROPANE, AND 17-23% PEG 3350, MICROBATCH, TEMPERATURE REMARK 280 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.65600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.65600 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 69.18000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 85.27550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 69.18000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 85.27550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.65600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 69.18000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 85.27550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.65600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 69.18000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 85.27550 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -48.65600 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F 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 APPLY THE FOLLOWING TO CHAINS: D, E, F REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 170.55100 REMARK 350 BIOMT3 2 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 50 REMARK 465 PRO A 51 REMARK 465 THR A 52 REMARK 465 GLU A 161 REMARK 465 HIS A 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 GLY B -4 REMARK 465 PRO B -3 REMARK 465 LEU B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ASN B 151 REMARK 465 ILE B 152 REMARK 465 MET D 50 REMARK 465 PRO D 51 REMARK 465 THR D 52 REMARK 465 HIS D 164 REMARK 465 HIS D 165 REMARK 465 HIS D 166 REMARK 465 HIS D 167 REMARK 465 GLY E -4 REMARK 465 PRO E -3 REMARK 465 LEU E -2 REMARK 465 GLY E -1 REMARK 465 SER E 0 REMARK 465 MET E 1 REMARK 465 ALA E 2 REMARK 465 ILE E 152 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 GLN A 55 -152.31 -95.67 REMARK 500 GLN A 104 80.12 -69.13 REMARK 500 GLU B 61 30.26 -96.89 REMARK 500 ASP B 93 -179.16 176.26 REMARK 500 LEU B 121 -54.74 -129.15 REMARK 500 ASN C 60 56.04 75.38 REMARK 500 ARG C 74 -102.21 -106.19 REMARK 500 GLN D 55 -152.86 -95.01 REMARK 500 GLN D 104 80.18 -68.96 REMARK 500 HIS D 162 41.07 82.44 REMARK 500 GLU E 61 30.02 -96.95 REMARK 500 ASP E 93 4.56 87.99 REMARK 500 GLN E 94 47.13 -91.27 REMARK 500 LEU E 121 -54.62 -129.01 REMARK 500 ASN E 150 -40.66 76.23 REMARK 500 ASN F 60 56.15 75.28 REMARK 500 ARG F 74 -103.15 -105.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 71 SG REMARK 620 2 CYS A 74 SG 100.9 REMARK 620 3 CYS A 91 SG 97.4 106.8 REMARK 620 4 CYS A 94 SG 122.2 119.8 106.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 86 SG REMARK 620 2 HIS A 88 NE2 96.7 REMARK 620 3 CYS A 106 SG 88.8 100.3 REMARK 620 4 ASP A 109 OD1 127.2 133.7 95.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 135 SG REMARK 620 2 CYS A 140 SG 91.1 REMARK 620 3 HIS A 152 NE2 101.3 125.3 REMARK 620 4 CYS A 156 SG 88.3 114.9 118.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 71 SG REMARK 620 2 CYS D 74 SG 100.8 REMARK 620 3 CYS D 91 SG 97.1 107.6 REMARK 620 4 CYS D 94 SG 122.1 119.9 106.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 86 SG REMARK 620 2 HIS D 88 NE2 96.5 REMARK 620 3 CYS D 106 SG 88.7 99.8 REMARK 620 4 ASP D 109 OD1 127.9 133.4 95.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 135 SG REMARK 620 2 CYS D 140 SG 88.7 REMARK 620 3 HIS D 152 NE2 91.2 128.6 REMARK 620 4 CYS D 156 SG 91.1 115.8 115.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VO0 RELATED DB: PDB DBREF 5VNZ A 50 167 PDB 5VNZ 5VNZ 50 167 DBREF 5VNZ B 1 152 UNP P61088 UBE2N_HUMAN 1 152 DBREF 5VNZ C 1 76 UNP P0CG47 UBB_HUMAN 1 76 DBREF 5VNZ D 50 167 PDB 5VNZ 5VNZ 50 167 DBREF 5VNZ E 1 152 UNP P61088 UBE2N_HUMAN 1 152 DBREF 5VNZ F 1 76 UNP P0CG47 UBB_HUMAN 1 76 SEQADV 5VNZ GLY B -4 UNP P61088 EXPRESSION TAG SEQADV 5VNZ PRO B -3 UNP P61088 EXPRESSION TAG SEQADV 5VNZ LEU B -2 UNP P61088 EXPRESSION TAG SEQADV 5VNZ GLY B -1 UNP P61088 EXPRESSION TAG SEQADV 5VNZ SER B 0 UNP P61088 EXPRESSION TAG SEQADV 5VNZ LYS B 87 UNP P61088 CYS 87 ENGINEERED MUTATION SEQADV 5VNZ THR B 92 UNP P61088 LYS 92 ENGINEERED MUTATION SEQADV 5VNZ GLN B 94 UNP P61088 LYS 94 ENGINEERED MUTATION SEQADV 5VNZ GLY E -4 UNP P61088 EXPRESSION TAG SEQADV 5VNZ PRO E -3 UNP P61088 EXPRESSION TAG SEQADV 5VNZ LEU E -2 UNP P61088 EXPRESSION TAG SEQADV 5VNZ GLY E -1 UNP P61088 EXPRESSION TAG SEQADV 5VNZ SER E 0 UNP P61088 EXPRESSION TAG SEQADV 5VNZ LYS E 87 UNP P61088 CYS 87 ENGINEERED MUTATION SEQADV 5VNZ THR E 92 UNP P61088 LYS 92 ENGINEERED MUTATION SEQADV 5VNZ GLN E 94 UNP P61088 LYS 94 ENGINEERED MUTATION SEQRES 1 A 118 MET PRO THR ASP GLN GLN GLY TYR ASP VAL GLU PHE ASP SEQRES 2 A 118 PRO PRO LEU GLU SER LYS TYR GLU CYS PRO ILE CYS LEU SEQRES 3 A 118 MET GLY LEU ARG SER ALA VAL GLN THR PRO CYS GLY HIS SEQRES 4 A 118 ARG PHE CYS ASP SER CYS ILE ARG LYS SER ILE ARG ASP SEQRES 5 A 118 THR GLY GLN LYS CYS PRO VAL ASP ASN GLU VAL LEU LEU SEQRES 6 A 118 GLU GLU GLN LEU PHE PRO ASP ASN PHE ALA LYS ARG GLU SEQRES 7 A 118 ILE LEU SER LEU THR VAL LYS CYS SER ASN PHE GLY CYS SEQRES 8 A 118 SER GLU LYS MET GLU LEU ARG GLN LEU GLU LYS HIS LEU SEQRES 9 A 118 SER GLN CYS ARG PHE ALA LEU GLU HIS HIS HIS HIS HIS SEQRES 10 A 118 HIS SEQRES 1 B 157 GLY PRO LEU GLY SER MET ALA GLY LEU PRO ARG ARG ILE SEQRES 2 B 157 ILE LYS GLU THR GLN ARG LEU LEU ALA GLU PRO VAL PRO SEQRES 3 B 157 GLY ILE LYS ALA GLU PRO ASP GLU SER ASN ALA ARG TYR SEQRES 4 B 157 PHE HIS VAL VAL ILE ALA GLY PRO GLN ASP SER PRO PHE SEQRES 5 B 157 GLU GLY GLY THR PHE LYS LEU GLU LEU PHE LEU PRO GLU SEQRES 6 B 157 GLU TYR PRO MET ALA ALA PRO LYS VAL ARG PHE MET THR SEQRES 7 B 157 LYS ILE TYR HIS PRO ASN VAL ASP LYS LEU GLY ARG ILE SEQRES 8 B 157 LYS LEU ASP ILE LEU THR ASP GLN TRP SER PRO ALA LEU SEQRES 9 B 157 GLN ILE ARG THR VAL LEU LEU SER ILE GLN ALA LEU LEU SEQRES 10 B 157 SER ALA PRO ASN PRO ASP ASP PRO LEU ALA ASN ASP VAL SEQRES 11 B 157 ALA GLU GLN TRP LYS THR ASN GLU ALA GLN ALA ILE GLU SEQRES 12 B 157 THR ALA ARG ALA TRP THR ARG LEU TYR ALA MET ASN ASN SEQRES 13 B 157 ILE SEQRES 1 C 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 D 118 MET PRO THR ASP GLN GLN GLY TYR ASP VAL GLU PHE ASP SEQRES 2 D 118 PRO PRO LEU GLU SER LYS TYR GLU CYS PRO ILE CYS LEU SEQRES 3 D 118 MET GLY LEU ARG SER ALA VAL GLN THR PRO CYS GLY HIS SEQRES 4 D 118 ARG PHE CYS ASP SER CYS ILE ARG LYS SER ILE ARG ASP SEQRES 5 D 118 THR GLY GLN LYS CYS PRO VAL ASP ASN GLU VAL LEU LEU SEQRES 6 D 118 GLU GLU GLN LEU PHE PRO ASP ASN PHE ALA LYS ARG GLU SEQRES 7 D 118 ILE LEU SER LEU THR VAL LYS CYS SER ASN PHE GLY CYS SEQRES 8 D 118 SER GLU LYS MET GLU LEU ARG GLN LEU GLU LYS HIS LEU SEQRES 9 D 118 SER GLN CYS ARG PHE ALA LEU GLU HIS HIS HIS HIS HIS SEQRES 10 D 118 HIS SEQRES 1 E 157 GLY PRO LEU GLY SER MET ALA GLY LEU PRO ARG ARG ILE SEQRES 2 E 157 ILE LYS GLU THR GLN ARG LEU LEU ALA GLU PRO VAL PRO SEQRES 3 E 157 GLY ILE LYS ALA GLU PRO ASP GLU SER ASN ALA ARG TYR SEQRES 4 E 157 PHE HIS VAL VAL ILE ALA GLY PRO GLN ASP SER PRO PHE SEQRES 5 E 157 GLU GLY GLY THR PHE LYS LEU GLU LEU PHE LEU PRO GLU SEQRES 6 E 157 GLU TYR PRO MET ALA ALA PRO LYS VAL ARG PHE MET THR SEQRES 7 E 157 LYS ILE TYR HIS PRO ASN VAL ASP LYS LEU GLY ARG ILE SEQRES 8 E 157 LYS LEU ASP ILE LEU THR ASP GLN TRP SER PRO ALA LEU SEQRES 9 E 157 GLN ILE ARG THR VAL LEU LEU SER ILE GLN ALA LEU LEU SEQRES 10 E 157 SER ALA PRO ASN PRO ASP ASP PRO LEU ALA ASN ASP VAL SEQRES 11 E 157 ALA GLU GLN TRP LYS THR ASN GLU ALA GLN ALA ILE GLU SEQRES 12 E 157 THR ALA ARG ALA TRP THR ARG LEU TYR ALA MET ASN ASN SEQRES 13 E 157 ILE SEQRES 1 F 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 F 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 F 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 F 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 F 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 F 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HET ZN A 201 1 HET ZN A 202 1 HET ZN A 203 1 HET ZN D 201 1 HET ZN D 202 1 HET ZN D 203 1 HETNAM ZN ZINC ION FORMUL 7 ZN 6(ZN 2+) HELIX 1 AA1 GLU A 66 GLU A 70 5 5 HELIX 2 AA2 CYS A 91 ASP A 101 1 11 HELIX 3 AA3 ASP A 121 SER A 130 1 10 HELIX 4 AA4 GLN A 148 CYS A 156 1 9 HELIX 5 AA5 PRO B 5 GLU B 18 1 14 HELIX 6 AA6 LEU B 88 ASP B 93 1 6 HELIX 7 AA7 GLN B 100 ALA B 114 1 15 HELIX 8 AA8 ALA B 122 ASN B 132 1 11 HELIX 9 AA9 ASN B 132 ALA B 148 1 17 HELIX 10 AB1 THR C 22 GLY C 35 1 14 HELIX 11 AB2 PRO C 37 GLN C 41 5 5 HELIX 12 AB3 THR C 55 ASN C 60 1 6 HELIX 13 AB4 GLU D 66 GLU D 70 5 5 HELIX 14 AB5 CYS D 91 ASP D 101 1 11 HELIX 15 AB6 ASP D 121 SER D 130 1 10 HELIX 16 AB7 GLN D 148 CYS D 156 1 9 HELIX 17 AB8 PRO E 5 GLU E 18 1 14 HELIX 18 AB9 LEU E 88 THR E 92 5 5 HELIX 19 AC1 GLN E 100 ALA E 114 1 15 HELIX 20 AC2 ALA E 122 ASN E 132 1 11 HELIX 21 AC3 ASN E 132 ALA E 148 1 17 HELIX 22 AC4 THR F 22 GLY F 35 1 14 HELIX 23 AC5 PRO F 37 GLN F 41 5 5 HELIX 24 AC6 THR F 55 ASN F 60 1 6 SHEET 1 AA1 3 ARG A 89 PHE A 90 0 SHEET 2 AA1 3 VAL A 82 GLN A 83 -1 N VAL A 82 O PHE A 90 SHEET 3 AA1 3 PHE A 119 PRO A 120 -1 O PHE A 119 N GLN A 83 SHEET 1 AA2 2 THR A 132 LYS A 134 0 SHEET 2 AA2 2 LYS A 143 GLU A 145 -1 O MET A 144 N VAL A 133 SHEET 1 AA3 4 ILE B 23 PRO B 27 0 SHEET 2 AA3 4 TYR B 34 ALA B 40 -1 O HIS B 36 N GLU B 26 SHEET 3 AA3 4 THR B 51 PHE B 57 -1 O LEU B 54 N VAL B 37 SHEET 4 AA3 4 LYS B 68 PHE B 71 -1 O ARG B 70 N GLU B 55 SHEET 1 AA4 5 THR C 12 GLU C 16 0 SHEET 2 AA4 5 GLN C 2 LYS C 6 -1 N VAL C 5 O ILE C 13 SHEET 3 AA4 5 SER C 65 VAL C 70 1 O LEU C 67 N PHE C 4 SHEET 4 AA4 5 ARG C 42 ILE C 44 -1 N ILE C 44 O HIS C 68 SHEET 5 AA4 5 GLN C 49 LEU C 50 -1 O LEU C 50 N LEU C 43 SHEET 1 AA5 3 ARG D 89 PHE D 90 0 SHEET 2 AA5 3 VAL D 82 GLN D 83 -1 N VAL D 82 O PHE D 90 SHEET 3 AA5 3 PHE D 119 PRO D 120 -1 O PHE D 119 N GLN D 83 SHEET 1 AA6 2 THR D 132 LYS D 134 0 SHEET 2 AA6 2 LYS D 143 GLU D 145 -1 O MET D 144 N VAL D 133 SHEET 1 AA7 4 ILE E 23 PRO E 27 0 SHEET 2 AA7 4 TYR E 34 ALA E 40 -1 O HIS E 36 N GLU E 26 SHEET 3 AA7 4 THR E 51 PHE E 57 -1 O LEU E 54 N VAL E 37 SHEET 4 AA7 4 LYS E 68 PHE E 71 -1 O ARG E 70 N GLU E 55 SHEET 1 AA8 5 THR F 12 GLU F 16 0 SHEET 2 AA8 5 GLN F 2 LYS F 6 -1 N VAL F 5 O ILE F 13 SHEET 3 AA8 5 SER F 65 VAL F 70 1 O LEU F 67 N PHE F 4 SHEET 4 AA8 5 ARG F 42 ILE F 44 -1 N ILE F 44 O HIS F 68 SHEET 5 AA8 5 GLN F 49 LEU F 50 -1 O LEU F 50 N LEU F 43 LINK NZ LYS B 87 C GLY C 76 1555 1555 1.35 LINK NZ LYS E 87 C GLY F 76 1555 1555 1.34 LINK SG CYS A 71 ZN ZN A 201 1555 1555 2.34 LINK SG CYS A 74 ZN ZN A 201 1555 1555 2.34 LINK SG CYS A 86 ZN ZN A 202 1555 1555 2.33 LINK NE2 HIS A 88 ZN ZN A 202 1555 1555 1.90 LINK SG CYS A 91 ZN ZN A 201 1555 1555 2.33 LINK SG CYS A 94 ZN ZN A 201 1555 1555 2.34 LINK SG CYS A 106 ZN ZN A 202 1555 1555 2.33 LINK OD1 ASP A 109 ZN ZN A 202 1555 1555 2.37 LINK SG CYS A 135 ZN ZN A 203 1555 1555 2.32 LINK SG CYS A 140 ZN ZN A 203 1555 1555 2.34 LINK NE2 HIS A 152 ZN ZN A 203 1555 1555 2.16 LINK SG CYS A 156 ZN ZN A 203 1555 1555 2.34 LINK SG CYS D 71 ZN ZN D 201 1555 1555 2.34 LINK SG CYS D 74 ZN ZN D 201 1555 1555 2.34 LINK SG CYS D 86 ZN ZN D 202 1555 1555 2.34 LINK NE2 HIS D 88 ZN ZN D 202 1555 1555 1.90 LINK SG CYS D 91 ZN ZN D 201 1555 1555 2.33 LINK SG CYS D 94 ZN ZN D 201 1555 1555 2.34 LINK SG CYS D 106 ZN ZN D 202 1555 1555 2.33 LINK OD1 ASP D 109 ZN ZN D 202 1555 1555 2.38 LINK SG CYS D 135 ZN ZN D 203 1555 1555 2.35 LINK SG CYS D 140 ZN ZN D 203 1555 1555 2.34 LINK NE2 HIS D 152 ZN ZN D 203 1555 1555 2.16 LINK SG CYS D 156 ZN ZN D 203 1555 1555 2.34 CISPEP 1 ASP A 62 PRO A 63 0 -0.34 CISPEP 2 TYR B 62 PRO B 63 0 10.43 CISPEP 3 ASP D 62 PRO D 63 0 -0.50 CISPEP 4 TYR E 62 PRO E 63 0 10.42 SITE 1 AC1 4 CYS A 71 CYS A 74 CYS A 91 CYS A 94 SITE 1 AC2 5 CYS A 86 HIS A 88 CYS A 106 VAL A 108 SITE 2 AC2 5 ASP A 109 SITE 1 AC3 4 CYS A 135 CYS A 140 HIS A 152 CYS A 156 SITE 1 AC4 4 CYS D 71 CYS D 74 CYS D 91 CYS D 94 SITE 1 AC5 5 CYS D 86 HIS D 88 CYS D 106 VAL D 108 SITE 2 AC5 5 ASP D 109 SITE 1 AC6 4 CYS D 135 CYS D 140 HIS D 152 CYS D 156 CRYST1 138.360 170.551 97.312 90.00 90.00 90.00 C 2 2 21 16 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 0.007228 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005863 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010276 0.00000