HEADER LIGASE 21-OCT-19 6T7F TITLE RCR E3 LIGASE E2-UBIQUITIN TRANSTHIOLATION INTERMEDIATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE MYCBP2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MYC-BINDING PROTEIN 2,PROTEIN ASSOCIATED WITH MYC; COMPND 5 EC: 2.3.2.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D3; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: (E3-INDEPENDENT) E2 UBIQUITIN-CONJUGATING ENZYME D3,E2 COMPND 11 UBIQUITIN-CONJUGATING ENZYME D3,UBIQUITIN CARRIER PROTEIN D3, COMPND 12 UBIQUITIN-CONJUGATING ENZYME E2(17)KB 3,UBIQUITIN-CONJUGATING ENZYME COMPND 13 E2-17 KDA 3,UBIQUITIN-PROTEIN LIGASE D3; COMPND 14 EC: 2.3.2.23,2.3.2.24; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES; COMPND 17 MOL_ID: 3; COMPND 18 MOLECULE: POLYUBIQUITIN-C; COMPND 19 CHAIN: C; COMPND 20 ENGINEERED: YES; COMPND 21 OTHER_DETAILS: CHEMICALLY MODIFIED UBIQUITIN RESIDUES 1-73 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MYCBP2, KIAA0916, PAM; 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: UBE2D3, UBC5C, UBCH5C; 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: UBC; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RING-CYS-RELAY, RCR, ACTIVITY BASED PROBE, UBIQUITINATION, THREONINE KEYWDS 2 E3 LIGASE., LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR P.D.MABBITT,S.VIRDEE REVDAT 4 24-JAN-24 6T7F 1 REMARK REVDAT 3 28-OCT-20 6T7F 1 JRNL REVDAT 2 12-AUG-20 6T7F 1 JRNL REVDAT 1 05-AUG-20 6T7F 0 JRNL AUTH P.D.MABBITT,A.LORETO,M.A.DERY,A.J.FLETCHER,M.STANLEY, JRNL AUTH 2 K.C.PAO,N.T.WOOD,M.P.COLEMAN,S.VIRDEE JRNL TITL STRUCTURAL BASIS FOR RING-CYS-RELAY E3 LIGASE ACTIVITY AND JRNL TITL 2 ITS ROLE IN AXON INTEGRITY. JRNL REF NAT.CHEM.BIOL. V. 16 1227 2020 JRNL REFN ESSN 1552-4469 JRNL PMID 32747811 JRNL DOI 10.1038/S41589-020-0598-6 REMARK 2 REMARK 2 RESOLUTION. 2.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 2.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 15778 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 895 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) : 2.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.65 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1038 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.3450 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.4320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3657 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 78.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.62000 REMARK 3 B22 (A**2) : -2.62000 REMARK 3 B33 (A**2) : 8.52000 REMARK 3 B12 (A**2) : -1.31000 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): 1.042 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.329 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.260 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.324 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3789 ; 0.007 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5139 ; 1.514 ; 1.655 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 468 ; 7.796 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 194 ;29.456 ;21.443 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 597 ;19.106 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;19.620 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 497 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2939 ; 0.006 ; 0.020 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): 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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: U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6T7F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1292104956. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2737 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16676 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.580 REMARK 200 RESOLUTION RANGE LOW (A) : 48.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 17.60 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.4 REMARK 200 DATA REDUNDANCY IN SHELL : 9.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.2 REMARK 200 STARTING MODEL: 5O6C, 5EGG, 1UBQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.85 M SODIUM CITRATE, 100 MM SODIUM REMARK 280 CHLORIDE, 100 MM TRIS-HCL PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 89.50400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.67516 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 29.09200 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 89.50400 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 51.67516 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 29.09200 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 89.50400 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 51.67516 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 29.09200 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 89.50400 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 51.67516 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 29.09200 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 89.50400 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 51.67516 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 29.09200 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 89.50400 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 51.67516 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 29.09200 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 103.35032 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 58.18400 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 103.35032 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 58.18400 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 103.35032 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 58.18400 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 103.35032 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 58.18400 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 103.35032 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 58.18400 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 103.35032 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 58.18400 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL 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 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 GLY A 4380 REMARK 465 PRO A 4381 REMARK 465 LEU A 4382 REMARK 465 GLY A 4383 REMARK 465 SER A 4384 REMARK 465 ASP A 4385 REMARK 465 ALA A 4386 REMARK 465 ALA A 4637 REMARK 465 HIS A 4638 REMARK 465 THR A 4639 REMARK 465 PHE A 4640 REMARK 465 MET C 1 REMARK 465 LEU C 73 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A4388 CG OD1 OD2 REMARK 470 MET A4389 CG SD CE REMARK 470 MET A4391 CG SD CE REMARK 470 LYS A4478 CG CD CE NZ REMARK 470 LYS A4508 CG CD CE NZ REMARK 470 LYS A4511 CG CD CE NZ REMARK 470 GLU A4523 CG CD OE1 OE2 REMARK 470 ASP A4529 CG OD1 OD2 REMARK 470 ARG A4545 CG CD NE CZ NH1 NH2 REMARK 470 GLN A4547 CG CD OE1 NE2 REMARK 470 ASN A4636 CG OD1 ND2 REMARK 470 LYS B 4 CG CD CE NZ REMARK 470 LYS B 66 CG CD CE NZ REMARK 470 GLU C 16 CG CD OE1 OE2 REMARK 470 GLU C 18 CG CD OE1 OE2 REMARK 470 LYS C 63 CG CD CE NZ REMARK 470 GLU C 64 CG CD OE1 OE2 REMARK 470 ARG C 72 CG CD NE CZ NH1 NH2 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 ILE A4392 -67.70 -91.40 REMARK 500 PRO A4402 126.43 -39.23 REMARK 500 SER A4409 -43.31 128.50 REMARK 500 ARG A4424 -136.98 54.81 REMARK 500 PRO A4438 -30.98 -31.73 REMARK 500 ILE A4439 -78.02 -105.08 REMARK 500 HIS A4446 147.40 -179.32 REMARK 500 LYS A4508 -75.10 -72.39 REMARK 500 CYS A4509 -157.16 -68.40 REMARK 500 ARG A4545 53.46 26.82 REMARK 500 LYS A4551 -84.49 -58.74 REMARK 500 THR A4575 -27.26 -144.26 REMARK 500 LEU B 13 -74.82 -80.17 REMARK 500 ALA B 14 0.46 -61.94 REMARK 500 ASP B 16 68.13 135.72 REMARK 500 PRO B 61 37.95 -99.59 REMARK 500 ARG B 90 -107.56 -126.75 REMARK 500 ASP B 112 90.46 -171.96 REMARK 500 ASP B 117 78.99 -116.62 REMARK 500 THR C 9 30.57 -93.03 REMARK 500 ASN C 60 30.90 71.23 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 A4701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A4390 SG REMARK 620 2 CYS A4393 SG 106.9 REMARK 620 3 HIS A4413 ND1 81.0 113.6 REMARK 620 4 CYS A4416 SG 135.1 96.0 124.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A4702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A4408 SG REMARK 620 2 HIS A4410 NE2 108.1 REMARK 620 3 CYS A4437 SG 96.9 125.6 REMARK 620 4 CYS A4440 SG 116.9 99.1 111.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A4703 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A4506 SG REMARK 620 2 CYS A4509 SG 95.4 REMARK 620 3 CYS A4537 SG 118.8 119.9 REMARK 620 4 CYS A4540 SG 104.2 123.4 95.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A4704 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A4549 SG REMARK 620 2 HIS A4552 ND1 115.3 REMARK 620 3 CYS A4631 SG 116.0 110.1 REMARK 620 4 CYS A4634 SG 129.0 89.7 92.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A4705 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A4561 SG REMARK 620 2 CYS A4564 SG 114.6 REMARK 620 3 CYS A4579 SG 109.1 102.6 REMARK 620 4 CYS A4582 SG 107.8 119.6 101.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A4706 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A4565 SG REMARK 620 2 CYS A4600 SG 119.7 REMARK 620 3 CYS A4614 SG 118.9 102.9 REMARK 620 4 HIS A4620 NE2 102.0 102.5 109.4 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 4701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 4702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 4703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 4704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 4705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 4706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LWZ B 201 DBREF 6T7F A 4385 4640 UNP O75592 MYCB2_HUMAN 4423 4678 DBREF 6T7F B 2 147 UNP P61077 UB2D3_HUMAN 2 147 DBREF 6T7F C 1 73 UNP P0CG48 UBC_HUMAN 1 73 SEQADV 6T7F GLY A 4380 UNP O75592 EXPRESSION TAG SEQADV 6T7F PRO A 4381 UNP O75592 EXPRESSION TAG SEQADV 6T7F LEU A 4382 UNP O75592 EXPRESSION TAG SEQADV 6T7F GLY A 4383 UNP O75592 EXPRESSION TAG SEQADV 6T7F SER A 4384 UNP O75592 EXPRESSION TAG SEQADV 6T7F GLY B -2 UNP P61077 EXPRESSION TAG SEQADV 6T7F PRO B -1 UNP P61077 EXPRESSION TAG SEQADV 6T7F GLY B 0 UNP P61077 EXPRESSION TAG SEQADV 6T7F SER B 1 UNP P61077 EXPRESSION TAG SEQADV 6T7F SER B 21 UNP P61077 CYS 21 ENGINEERED MUTATION SEQADV 6T7F ARG B 22 UNP P61077 SER 22 ENGINEERED MUTATION SEQADV 6T7F SER B 107 UNP P61077 CYS 107 ENGINEERED MUTATION SEQADV 6T7F SER B 111 UNP P61077 CYS 111 ENGINEERED MUTATION SEQRES 1 A 261 GLY PRO LEU GLY SER ASP ALA ASP ASP MET CYS MET ILE SEQRES 2 A 261 CYS PHE THR GLU ALA LEU SER ALA ALA PRO ALA ILE GLN SEQRES 3 A 261 LEU ASP CYS SER HIS ILE PHE HIS LEU GLN CYS CYS ARG SEQRES 4 A 261 ARG VAL LEU GLU ASN ARG TRP LEU GLY PRO ARG ILE THR SEQRES 5 A 261 PHE GLY PHE ILE SER CYS PRO ILE CYS LYS ASN LYS ILE SEQRES 6 A 261 ASN HIS ILE VAL LEU LYS ASP LEU LEU ASP PRO ILE LYS SEQRES 7 A 261 GLU LEU TYR GLU ASP VAL ARG ARG LYS ALA LEU MET ARG SEQRES 8 A 261 LEU GLU TYR GLU GLY LEU HIS LYS SER GLU ALA ILE THR SEQRES 9 A 261 THR PRO GLY VAL ARG PHE TYR ASN ASP PRO ALA GLY TYR SEQRES 10 A 261 ALA MET ASN ARG TYR ALA TYR TYR VAL CYS TYR LYS CYS SEQRES 11 A 261 ARG LYS ALA TYR PHE GLY GLY GLU ALA ARG CYS ASP ALA SEQRES 12 A 261 GLU ALA GLY ARG GLY ASP ASP TYR ASP PRO ARG GLU LEU SEQRES 13 A 261 ILE CYS GLY ALA CYS SER ASP VAL SER ARG ALA GLN MET SEQRES 14 A 261 CYS PRO LYS HIS GLY THR ASP PHE LEU GLU TYR LYS CYS SEQRES 15 A 261 ARG TYR CYS CYS SER VAL ALA VAL PHE PHE CYS PHE GLY SEQRES 16 A 261 THR THR HIS PHE CYS ASN ALA CYS HIS ASP ASP PHE GLN SEQRES 17 A 261 ARG MET THR SER ILE PRO LYS GLU GLU LEU PRO HIS CYS SEQRES 18 A 261 PRO ALA GLY PRO LYS GLY LYS GLN LEU GLU GLY THR GLU SEQRES 19 A 261 CYS PRO LEU HIS VAL VAL HIS PRO PRO THR GLY GLU GLU SEQRES 20 A 261 PHE ALA LEU GLY CYS GLY VAL CYS ARG ASN ALA HIS THR SEQRES 21 A 261 PHE SEQRES 1 B 150 GLY PRO GLY SER ALA LEU LYS ARG ILE ASN LYS GLU LEU SEQRES 2 B 150 SER ASP LEU ALA ARG ASP PRO PRO ALA GLN SER ARG ALA SEQRES 3 B 150 GLY PRO VAL GLY ASP ASP MET PHE HIS TRP GLN ALA THR SEQRES 4 B 150 ILE MET GLY PRO ASN ASP SER PRO TYR GLN GLY GLY VAL SEQRES 5 B 150 PHE PHE LEU THR ILE HIS PHE PRO THR ASP TYR PRO PHE SEQRES 6 B 150 LYS PRO PRO LYS VAL ALA PHE THR THR ARG ILE TYR HIS SEQRES 7 B 150 PRO ASN ILE ASN SER ASN GLY SER ILE CYS LEU ASP ILE SEQRES 8 B 150 LEU ARG SER GLN TRP SER PRO ALA LEU THR ILE SER LYS SEQRES 9 B 150 VAL LEU LEU SER ILE SER SER LEU LEU SER ASP PRO ASN SEQRES 10 B 150 PRO ASP ASP PRO LEU VAL PRO GLU ILE ALA ARG ILE TYR SEQRES 11 B 150 LYS THR ASP ARG ASP LYS TYR ASN ARG ILE SER ARG GLU SEQRES 12 B 150 TRP THR GLN LYS TYR ALA MET SEQRES 1 C 73 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 73 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 73 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 73 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 73 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 73 THR LEU HIS LEU VAL LEU ARG LEU HET ZN A4701 1 HET ZN A4702 1 HET ZN A4703 1 HET ZN A4704 1 HET ZN A4705 1 HET ZN A4706 1 HET LWZ B 201 13 HETNAM ZN ZINC ION HETNAM LWZ 3,3-BIS(SULFANYL)-~{N}-(1~{H}-1,2,3-TRIAZOL-4- HETNAM 2 LWZ YLMETHYL)PROPANAMIDE FORMUL 4 ZN 6(ZN 2+) FORMUL 10 LWZ C6 H10 N4 O S2 FORMUL 11 HOH *41(H2 O) HELIX 1 AA1 ALA A 4397 ALA A 4401 5 5 HELIX 2 AA2 LEU A 4414 ARG A 4424 1 11 HELIX 3 AA3 PHE A 4432 SER A 4436 5 5 HELIX 4 AA4 HIS A 4446 VAL A 4448 5 3 HELIX 5 AA5 LEU A 4449 GLU A 4474 1 26 HELIX 6 AA6 SER A 4479 THR A 4484 1 6 HELIX 7 AA7 ASP A 4492 ARG A 4500 1 9 HELIX 8 AA8 ASP A 4531 LEU A 4535 5 5 HELIX 9 AA9 CYS A 4537 ASP A 4542 5 6 HELIX 10 AB1 CYS A 4579 ASP A 4585 1 7 HELIX 11 AB2 ASP A 4585 ILE A 4592 1 8 HELIX 12 AB3 PRO A 4593 LEU A 4597 5 5 HELIX 13 AB4 GLY A 4603 LYS A 4607 5 5 HELIX 14 AB5 GLY A 4632 ASN A 4636 1 5 HELIX 15 AB6 PRO B -1 ALA B 14 1 16 HELIX 16 AB7 LEU B 86 ARG B 90 5 5 HELIX 17 AB8 THR B 98 ASP B 112 1 15 HELIX 18 AB9 VAL B 120 ASP B 130 1 11 HELIX 19 AC1 ASP B 130 ALA B 146 1 17 HELIX 20 AC2 THR C 22 GLY C 35 1 14 HELIX 21 AC3 PRO C 37 ASP C 39 5 3 SHEET 1 AA1 2 ALA A4403 GLN A4405 0 SHEET 2 AA1 2 ILE A4411 HIS A4413 -1 O PHE A4412 N ILE A4404 SHEET 1 AA2 3 ARG A4429 ILE A4430 0 SHEET 2 AA2 3 TYR A4501 VAL A4505 -1 O TYR A4503 N ILE A4430 SHEET 3 AA2 3 ALA A4512 GLU A4517 -1 O GLY A4515 N ALA A4502 SHEET 1 AA3 2 LEU A4557 TYR A4559 0 SHEET 2 AA3 2 ALA A4628 CYS A4631 -1 O LEU A4629 N GLU A4558 SHEET 1 AA4 2 PHE A4570 CYS A4572 0 SHEET 2 AA4 2 THR A4576 PHE A4578 -1 O PHE A4578 N PHE A4570 SHEET 1 AA5 4 SER B 21 PRO B 25 0 SHEET 2 AA5 4 HIS B 32 MET B 38 -1 O GLN B 34 N GLY B 24 SHEET 3 AA5 4 VAL B 49 HIS B 55 -1 O LEU B 52 N ALA B 35 SHEET 4 AA5 4 LYS B 66 PHE B 69 -1 O LYS B 66 N HIS B 55 SHEET 1 AA6 5 THR C 12 LEU C 15 0 SHEET 2 AA6 5 ILE C 3 THR C 7 -1 N ILE C 3 O LEU C 15 SHEET 3 AA6 5 THR C 66 LEU C 71 1 O LEU C 67 N LYS C 6 SHEET 4 AA6 5 GLN C 41 PHE C 45 -1 N ARG C 42 O VAL C 70 SHEET 5 AA6 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 LINK CB CYS A4520 S03 LWZ B 201 1555 1555 1.76 LINK CB CYS B 85 S01 LWZ B 201 1555 1555 1.86 LINK SG CYS A4390 ZN ZN A4701 1555 1555 2.33 LINK SG CYS A4393 ZN ZN A4701 1555 1555 2.33 LINK SG CYS A4408 ZN ZN A4702 1555 1555 2.33 LINK NE2 HIS A4410 ZN ZN A4702 1555 1555 1.88 LINK ND1 HIS A4413 ZN ZN A4701 1555 1555 2.17 LINK SG CYS A4416 ZN ZN A4701 1555 1555 2.32 LINK SG CYS A4437 ZN ZN A4702 1555 1555 2.34 LINK SG CYS A4440 ZN ZN A4702 1555 1555 2.36 LINK SG CYS A4506 ZN ZN A4703 1555 1555 2.38 LINK SG CYS A4509 ZN ZN A4703 1555 1555 2.31 LINK SG CYS A4537 ZN ZN A4703 1555 1555 2.34 LINK SG CYS A4540 ZN ZN A4703 1555 1555 2.33 LINK SG CYS A4549 ZN ZN A4704 1555 1555 2.35 LINK ND1 HIS A4552 ZN ZN A4704 1555 1555 2.18 LINK SG CYS A4561 ZN ZN A4705 1555 1555 2.32 LINK SG CYS A4564 ZN ZN A4705 1555 1555 2.33 LINK SG CYS A4565 ZN ZN A4706 1555 1555 2.33 LINK SG CYS A4579 ZN ZN A4705 1555 1555 2.29 LINK SG CYS A4582 ZN ZN A4705 1555 1555 2.33 LINK SG CYS A4600 ZN ZN A4706 1555 1555 2.26 LINK SG CYS A4614 ZN ZN A4706 1555 1555 2.31 LINK NE2 HIS A4620 ZN ZN A4706 1555 1555 2.07 LINK SG CYS A4631 ZN ZN A4704 1555 1555 2.34 LINK SG CYS A4634 ZN ZN A4704 1555 1555 2.27 CISPEP 1 CYS A 4600 PRO A 4601 0 0.84 CISPEP 2 TYR B 60 PRO B 61 0 -2.47 SITE 1 AC1 4 CYS A4390 CYS A4393 HIS A4413 CYS A4416 SITE 1 AC2 4 CYS A4408 HIS A4410 CYS A4437 CYS A4440 SITE 1 AC3 4 CYS A4506 CYS A4509 CYS A4537 CYS A4540 SITE 1 AC4 4 CYS A4549 HIS A4552 CYS A4631 CYS A4634 SITE 1 AC5 4 CYS A4561 CYS A4564 CYS A4579 CYS A4582 SITE 1 AC6 4 CYS A4565 CYS A4600 CYS A4614 HIS A4620 SITE 1 AC7 6 CYS A4520 ASN B 77 CYS B 85 ASN B 114 SITE 2 AC7 6 ASP B 117 ARG C 72 CRYST1 179.008 179.008 87.276 90.00 90.00 120.00 H 3 2 18 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 0.005586 0.003225 0.000000 0.00000 SCALE2 0.000000 0.006451 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011458 0.00000