HEADER LIGASE 20-OCT-14 4V3K
TITLE RNF38-UBCH5B-UB COMPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D2;
COMPND 3 CHAIN: A, D;
COMPND 4 FRAGMENT: RESIDUES 2-147;
COMPND 5 SYNONYM: UBIQUITIN CARRIER PROTEIN D2, UBIQUITIN-CONJUGATING ENZYME
COMPND 6 E2(17)KB 2, UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2, UBIQUITIN-
COMPND 7 PROTEIN LIGASE D2, P53-REGULATED UBIQUITIN-CONJUGATING ENZYME 1,
COMPND 8 UBCH5B;
COMPND 9 EC: 6.3.2.19;
COMPND 10 ENGINEERED: YES;
COMPND 11 MUTATION: YES;
COMPND 12 OTHER_DETAILS: LYS85 IN CHAINS A AND D IS COVALENTLY LINKED TO GLY76
COMPND 13 IN CHAINS B AND E, RESPECTIVELY.;
COMPND 14 MOL_ID: 2;
COMPND 15 MOLECULE: POLYUBIQUITIN-C;
COMPND 16 CHAIN: B, E;
COMPND 17 FRAGMENT: RESIDUES 77-152;
COMPND 18 SYNONYM: UBIQUITIN;
COMPND 19 ENGINEERED: YES;
COMPND 20 OTHER_DETAILS: LYS85 IN CHAINS A AND D IS COVALENTLY LINKED TO GLY76
COMPND 21 IN CHAINS B AND E, RESPECTIVELY.;
COMPND 22 MOL_ID: 3;
COMPND 23 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE RNF38;
COMPND 24 CHAIN: C, F;
COMPND 25 FRAGMENT: RESIDUES 439-515;
COMPND 26 SYNONYM: RING FINGER PROTEIN 38, RNF38;
COMPND 27 EC: 6.3.2.19;
COMPND 28 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 8 MOL_ID: 2;
SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 10 ORGANISM_COMMON: HUMAN;
SOURCE 11 ORGANISM_TAXID: 9606;
SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 15 MOL_ID: 3;
SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 17 ORGANISM_COMMON: HUMAN;
SOURCE 18 ORGANISM_TAXID: 9606;
SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 20 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 21 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)
KEYWDS RING E3, E2, UBIQUITIN, LIGASE
EXPDTA X-RAY DIFFRACTION
AUTHOR L.BUETOW,M.GABRIELSEN,N.G.ANTHONY,H.DOU,A.PATEL,H.AITKENHEAD,
AUTHOR 2 G.J.SIBBET,B.O.SMITH,D.T.HUANG
REVDAT 4 10-JAN-24 4V3K 1 REMARK
REVDAT 3 31-JUL-19 4V3K 1 REMARK LINK
REVDAT 2 29-APR-15 4V3K 1 JRNL
REVDAT 1 08-APR-15 4V3K 0
JRNL AUTH L.BUETOW,M.GABRIELSEN,N.G.ANTHONY,H.DOU,A.PATEL,
JRNL AUTH 2 H.AITKENHEAD,G.J.SIBBET,B.O.SMITH,D.T.HUANG
JRNL TITL ACTIVATION OF A PRIMED RING E3-E2-UBIQUITIN COMPLEX BY
JRNL TITL 2 NON-COVALENT UBIQUITIN.
JRNL REF MOL.CELL V. 58 297 2015
JRNL REFN ISSN 1097-2765
JRNL PMID 25801170
JRNL DOI 10.1016/J.MOLCEL.2015.02.017
REMARK 2
REMARK 2 RESOLUTION. 2.04 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.91
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 44936
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.183
REMARK 3 R VALUE (WORKING SET) : 0.181
REMARK 3 FREE R VALUE : 0.223
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 2269
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 34.9101 - 5.1354 1.00 2909 127 0.2063 0.2003
REMARK 3 2 5.1354 - 4.0781 1.00 2747 150 0.1480 0.1770
REMARK 3 3 4.0781 - 3.5632 1.00 2682 146 0.1603 0.1789
REMARK 3 4 3.5632 - 3.2377 1.00 2677 156 0.1796 0.2128
REMARK 3 5 3.2377 - 3.0057 1.00 2688 127 0.1855 0.2399
REMARK 3 6 3.0057 - 2.8286 1.00 2642 151 0.1994 0.2570
REMARK 3 7 2.8286 - 2.6870 1.00 2666 135 0.1833 0.2363
REMARK 3 8 2.6870 - 2.5701 1.00 2653 144 0.1888 0.2782
REMARK 3 9 2.5701 - 2.4712 1.00 2652 143 0.1876 0.2609
REMARK 3 10 2.4712 - 2.3859 1.00 2628 132 0.1838 0.2550
REMARK 3 11 2.3859 - 2.3113 1.00 2635 138 0.1867 0.2534
REMARK 3 12 2.3113 - 2.2453 1.00 2632 143 0.1718 0.2318
REMARK 3 13 2.2453 - 2.1862 1.00 2622 132 0.1851 0.2660
REMARK 3 14 2.1862 - 2.1328 1.00 2613 147 0.1863 0.2890
REMARK 3 15 2.1328 - 2.0844 1.00 2627 130 0.2007 0.2533
REMARK 3 16 2.0844 - 2.0400 1.00 2594 168 0.2009 0.2621
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : 0.37
REMARK 3 B_SOL : 37.74
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.630
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.980
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 24.56
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.70
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 3.89380
REMARK 3 B22 (A**2) : 3.89380
REMARK 3 B33 (A**2) : -7.78760
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 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.008 4847
REMARK 3 ANGLE : 1.184 6598
REMARK 3 CHIRALITY : 0.095 735
REMARK 3 PLANARITY : 0.007 862
REMARK 3 DIHEDRAL : 14.266 1839
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: IN CHAIN C, RESIDUES 389 AND 465 ARE
REMARK 3 DISORDERED. IN CHAIN F, RESIDUE 389 AND 460-465 ARE DISORDERED.
REMARK 3 RESIDUES WITH POOR SIDE CHAIN ELECTRON DENSITY WERE BUILT AS
REMARK 3 ALANINE.
REMARK 4
REMARK 4 4V3K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-OCT-14.
REMARK 100 THE DEPOSITION ID IS D_1290062042.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-JUL-13
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 : DIAMOND
REMARK 200 BEAMLINE : I24
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97780
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 : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44936
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040
REMARK 200 RESOLUTION RANGE LOW (A) : 34.900
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 9.400
REMARK 200 R MERGE (I) : 0.12000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 9.70
REMARK 200 R MERGE FOR SHELL (I) : 0.82000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.800
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 ENTRIES 3ZNI AND 1X4J
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 50.33
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS-HCL, PH 8.5 AND 2.3 M
REMARK 280 AMMONIUM SULFATE
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2
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 -Y+1/2,X+1/2,Z+1/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-Z+1/2
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 35.34500
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 69.81000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 69.81000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.67250
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 69.81000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 69.81000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 53.01750
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 69.81000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 69.81000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.67250
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 69.81000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 69.81000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 53.01750
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 35.34500
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: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3950 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 13840 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.6 KCAL/MOL
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
REMARK 350 BIOMOLECULE: 2
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: 4180 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 14870 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 B -4
REMARK 465 SER B -3
REMARK 465 GLY B -2
REMARK 465 GLY B -1
REMARK 465 GLY C 387
REMARK 465 SER C 388
REMARK 465 THR C 389
REMARK 465 GLU C 465
REMARK 465 GLY E -4
REMARK 465 SER E -3
REMARK 465 GLY E -2
REMARK 465 GLY E -1
REMARK 465 GLY F 387
REMARK 465 SER F 388
REMARK 465 THR F 389
REMARK 465 VAL F 460
REMARK 465 HIS F 461
REMARK 465 ARG F 462
REMARK 465 ASP F 463
REMARK 465 SER F 464
REMARK 465 GLU F 465
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 A 42 CG OD1 OD2
REMARK 470 GLU B 16 CG CD OE1 OE2
REMARK 470 GLU B 24 CG CD OE1 OE2
REMARK 470 ARG B 74 CG CD NE CZ NH1 NH2
REMARK 470 LYS C 390 CG CD CE NZ
REMARK 470 ASN C 404 CG OD1 ND2
REMARK 470 ARG C 423 CG CD NE CZ NH1 NH2
REMARK 470 LYS C 438 CG CD CE NZ
REMARK 470 LYS C 445 CG CD CE NZ
REMARK 470 ARG C 448 CG CD NE CZ NH1 NH2
REMARK 470 ASP C 463 CG OD1 OD2
REMARK 470 SER C 464 OG
REMARK 470 LYS D 4 CG CD CE NZ
REMARK 470 GLU D 122 CG CD OE1 OE2
REMARK 470 ARG D 125 CG CD NE CZ NH1 NH2
REMARK 470 GLU E 24 CG CD OE1 OE2
REMARK 470 LYS F 390 CG CD CE NZ
REMARK 470 GLN F 395 CG CD OE1 NE2
REMARK 470 ASN F 405 CG OD1 ND2
REMARK 470 GLN F 407 CG CD OE1 NE2
REMARK 470 SER F 408 OG
REMARK 470 ARG F 423 CG CD NE CZ NH1 NH2
REMARK 470 LYS F 445 CG CD CE NZ
REMARK 470 ARG F 448 CG CD NE CZ NH1 NH2
REMARK 470 GLU F 459 CG CD OE1 OE2
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 NZ LYS A 85 C GLY B 76 1.34
REMARK 500 NZ LYS D 85 C GLY E 76 1.35
REMARK 500 O HOH E 2005 O HOH E 2019 2.05
REMARK 500 NH2 ARG C 462 O HOH B 2018 2.13
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 GLN A 20 -1.52 76.90
REMARK 500 ASP A 42 -1.66 68.84
REMARK 500 PRO A 61 42.71 -93.18
REMARK 500 HIS A 75 140.58 -174.90
REMARK 500 ARG A 90 -88.26 -125.46
REMARK 500 GLU B 64 -1.51 74.77
REMARK 500 ARG C 423 -5.58 79.22
REMARK 500 ASN C 432 -0.27 81.64
REMARK 500 ARG C 454 -0.82 69.02
REMARK 500 PRO D 61 42.38 -93.95
REMARK 500 HIS D 75 141.70 -176.07
REMARK 500 ARG D 90 -89.68 -125.33
REMARK 500 GLU E 64 -0.85 80.22
REMARK 500 ARG F 423 -5.84 82.37
REMARK 500 ASN F 432 -0.68 83.64
REMARK 500 ARG F 454 -0.38 71.24
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 C1465 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS C 413 SG
REMARK 620 2 CYS C 416 SG 110.1
REMARK 620 3 HIS C 436 ND1 102.1 91.4
REMARK 620 4 CYS C 439 SG 113.3 116.4 120.9
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN C1466 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS C 431 SG
REMARK 620 2 HIS C 433 ND1 108.6
REMARK 620 3 CYS C 450 SG 105.1 108.5
REMARK 620 4 CYS C 453 SG 109.5 111.4 113.6
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN F1460 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS F 413 SG
REMARK 620 2 CYS F 416 SG 109.8
REMARK 620 3 HIS F 436 ND1 100.9 93.1
REMARK 620 4 CYS F 439 SG 116.1 113.4 120.6
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN F1461 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS F 431 SG
REMARK 620 2 HIS F 433 ND1 109.1
REMARK 620 3 CYS F 450 SG 102.9 110.0
REMARK 620 4 CYS F 453 SG 106.8 111.0 116.3
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 CL A 1148
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1149
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1150
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1151
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1077
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1078
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL D 1149
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL D 1150
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO D 1151
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO E 1077
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 1465
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 1466
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN F 1460
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN F 1461
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4V3L RELATED DB: PDB
REMARK 900 E3-E2-UB
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 N-TERMINAL METHIONINE IS CLEAVED DURING PURIFICATION.
REMARK 999 SER22 IS MUTATED TO ARGININE. CYS85 IS MUTATED TO LYSINE.
REMARK 999 CONTAINS GSGGS AT THE N-TERMINUS FROM CLONING
REMARK 999 CONTAINS RESIDUES 389-465 AND GS AT THE N-TERMINUS DUE TO
REMARK 999 CLONING
DBREF 4V3K A 2 147 UNP P62837 UB2D2_HUMAN 2 147
DBREF 4V3K B 1 76 UNP P0CG48 UBC_HUMAN 77 152
DBREF 4V3K C 389 465 UNP Q9H0F5 RNF38_HUMAN 439 515
DBREF 4V3K D 2 147 UNP P62837 UB2D2_HUMAN 2 147
DBREF 4V3K E 1 76 UNP P0CG48 UBC_HUMAN 77 152
DBREF 4V3K F 389 465 UNP Q9H0F5 RNF38_HUMAN 439 515
SEQADV 4V3K ARG A 22 UNP P62837 SER 22 ENGINEERED MUTATION
SEQADV 4V3K LYS A 85 UNP P62837 CYS 85 ENGINEERED MUTATION
SEQADV 4V3K GLY B -4 UNP P0CG48 EXPRESSION TAG
SEQADV 4V3K SER B -3 UNP P0CG48 EXPRESSION TAG
SEQADV 4V3K GLY B -2 UNP P0CG48 EXPRESSION TAG
SEQADV 4V3K GLY B -1 UNP P0CG48 EXPRESSION TAG
SEQADV 4V3K SER B 0 UNP P0CG48 EXPRESSION TAG
SEQADV 4V3K GLY C 387 UNP Q9H0F5 EXPRESSION TAG
SEQADV 4V3K SER C 388 UNP Q9H0F5 EXPRESSION TAG
SEQADV 4V3K ARG D 22 UNP P62837 SER 22 ENGINEERED MUTATION
SEQADV 4V3K LYS D 85 UNP P62837 CYS 85 ENGINEERED MUTATION
SEQADV 4V3K GLY E -4 UNP P0CG48 EXPRESSION TAG
SEQADV 4V3K SER E -3 UNP P0CG48 EXPRESSION TAG
SEQADV 4V3K GLY E -2 UNP P0CG48 EXPRESSION TAG
SEQADV 4V3K GLY E -1 UNP P0CG48 EXPRESSION TAG
SEQADV 4V3K SER E 0 UNP P0CG48 EXPRESSION TAG
SEQADV 4V3K GLY F 387 UNP Q9H0F5 EXPRESSION TAG
SEQADV 4V3K SER F 388 UNP Q9H0F5 EXPRESSION TAG
SEQRES 1 A 146 ALA LEU LYS ARG ILE HIS LYS GLU LEU ASN ASP LEU ALA
SEQRES 2 A 146 ARG ASP PRO PRO ALA GLN CYS ARG ALA GLY PRO VAL GLY
SEQRES 3 A 146 ASP ASP MET PHE HIS TRP GLN ALA THR ILE MET GLY PRO
SEQRES 4 A 146 ASN ASP SER PRO TYR GLN GLY GLY VAL PHE PHE LEU THR
SEQRES 5 A 146 ILE HIS PHE PRO THR ASP TYR PRO PHE LYS PRO PRO LYS
SEQRES 6 A 146 VAL ALA PHE THR THR ARG ILE TYR HIS PRO ASN ILE ASN
SEQRES 7 A 146 SER ASN GLY SER ILE LYS LEU ASP ILE LEU ARG SER GLN
SEQRES 8 A 146 TRP SER PRO ALA LEU THR ILE SER LYS VAL LEU LEU SER
SEQRES 9 A 146 ILE CYS SER LEU LEU CYS ASP PRO ASN PRO ASP ASP PRO
SEQRES 10 A 146 LEU VAL PRO GLU ILE ALA ARG ILE TYR LYS THR ASP ARG
SEQRES 11 A 146 GLU LYS TYR ASN ARG ILE ALA ARG GLU TRP THR GLN LYS
SEQRES 12 A 146 TYR ALA MET
SEQRES 1 B 81 GLY SER GLY GLY SER MET GLN ILE PHE VAL LYS THR LEU
SEQRES 2 B 81 THR GLY LYS THR ILE THR LEU GLU VAL GLU PRO SER ASP
SEQRES 3 B 81 THR ILE GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU
SEQRES 4 B 81 GLY ILE PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY
SEQRES 5 B 81 LYS GLN LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN
SEQRES 6 B 81 ILE GLN LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU
SEQRES 7 B 81 ARG GLY GLY
SEQRES 1 C 79 GLY SER THR LYS ALA ASP ILE GLU GLN LEU PRO SER TYR
SEQRES 2 C 79 ARG PHE ASN PRO ASN ASN HIS GLN SER GLU GLN THR LEU
SEQRES 3 C 79 CYS VAL VAL CYS MET CYS ASP PHE GLU SER ARG GLN LEU
SEQRES 4 C 79 LEU ARG VAL LEU PRO CYS ASN HIS GLU PHE HIS ALA LYS
SEQRES 5 C 79 CYS VAL ASP LYS TRP LEU LYS ALA ASN ARG THR CYS PRO
SEQRES 6 C 79 ILE CYS ARG ALA ASP ALA SER GLU VAL HIS ARG ASP SER
SEQRES 7 C 79 GLU
SEQRES 1 D 146 ALA LEU LYS ARG ILE HIS LYS GLU LEU ASN ASP LEU ALA
SEQRES 2 D 146 ARG ASP PRO PRO ALA GLN CYS ARG ALA GLY PRO VAL GLY
SEQRES 3 D 146 ASP ASP MET PHE HIS TRP GLN ALA THR ILE MET GLY PRO
SEQRES 4 D 146 ASN ASP SER PRO TYR GLN GLY GLY VAL PHE PHE LEU THR
SEQRES 5 D 146 ILE HIS PHE PRO THR ASP TYR PRO PHE LYS PRO PRO LYS
SEQRES 6 D 146 VAL ALA PHE THR THR ARG ILE TYR HIS PRO ASN ILE ASN
SEQRES 7 D 146 SER ASN GLY SER ILE LYS LEU ASP ILE LEU ARG SER GLN
SEQRES 8 D 146 TRP SER PRO ALA LEU THR ILE SER LYS VAL LEU LEU SER
SEQRES 9 D 146 ILE CYS SER LEU LEU CYS ASP PRO ASN PRO ASP ASP PRO
SEQRES 10 D 146 LEU VAL PRO GLU ILE ALA ARG ILE TYR LYS THR ASP ARG
SEQRES 11 D 146 GLU LYS TYR ASN ARG ILE ALA ARG GLU TRP THR GLN LYS
SEQRES 12 D 146 TYR ALA MET
SEQRES 1 E 81 GLY SER GLY GLY SER MET GLN ILE PHE VAL LYS THR LEU
SEQRES 2 E 81 THR GLY LYS THR ILE THR LEU GLU VAL GLU PRO SER ASP
SEQRES 3 E 81 THR ILE GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU
SEQRES 4 E 81 GLY ILE PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY
SEQRES 5 E 81 LYS GLN LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN
SEQRES 6 E 81 ILE GLN LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU
SEQRES 7 E 81 ARG GLY GLY
SEQRES 1 F 79 GLY SER THR LYS ALA ASP ILE GLU GLN LEU PRO SER TYR
SEQRES 2 F 79 ARG PHE ASN PRO ASN ASN HIS GLN SER GLU GLN THR LEU
SEQRES 3 F 79 CYS VAL VAL CYS MET CYS ASP PHE GLU SER ARG GLN LEU
SEQRES 4 F 79 LEU ARG VAL LEU PRO CYS ASN HIS GLU PHE HIS ALA LYS
SEQRES 5 F 79 CYS VAL ASP LYS TRP LEU LYS ALA ASN ARG THR CYS PRO
SEQRES 6 F 79 ILE CYS ARG ALA ASP ALA SER GLU VAL HIS ARG ASP SER
SEQRES 7 F 79 GLU
HET CL A1148 1
HET CL A1149 1
HET CL A1150 1
HET EDO A1151 4
HET EDO B1077 4
HET EDO B1078 4
HET ZN C1465 1
HET ZN C1466 1
HET CL D1148 1
HET CL D1149 1
HET CL D1150 1
HET EDO D1151 4
HET EDO E1077 4
HET ZN F1460 1
HET ZN F1461 1
HETNAM CL CHLORIDE ION
HETNAM EDO 1,2-ETHANEDIOL
HETNAM ZN ZINC ION
HETSYN EDO ETHYLENE GLYCOL
FORMUL 7 CL 6(CL 1-)
FORMUL 10 EDO 5(C2 H6 O2)
FORMUL 13 ZN 4(ZN 2+)
FORMUL 22 HOH *368(H2 O)
HELIX 1 1 ALA A 2 ASP A 16 1 15
HELIX 2 2 ASP A 87 ARG A 90 5 4
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
HELIX 6 6 THR B 22 GLY B 35 1 14
HELIX 7 7 PRO B 37 ASP B 39 5 3
HELIX 8 8 LEU B 56 ASN B 60 5 5
HELIX 9 9 LYS C 390 LEU C 396 1 7
HELIX 10 10 ALA C 437 ASN C 447 1 11
HELIX 11 11 ALA D 2 ASP D 16 1 15
HELIX 12 12 ASP D 87 ARG D 90 5 4
HELIX 13 13 THR D 98 CYS D 111 1 14
HELIX 14 14 VAL D 120 ASP D 130 1 11
HELIX 15 15 ASP D 130 ALA D 146 1 17
HELIX 16 16 THR E 22 GLY E 35 1 14
HELIX 17 17 PRO E 37 ASP E 39 5 3
HELIX 18 18 LEU E 56 ASN E 60 5 5
HELIX 19 19 LYS F 390 LEU F 396 1 7
HELIX 20 20 ALA F 437 ASN F 447 1 11
SHEET 1 AA 4 CYS A 21 GLY A 24 0
SHEET 2 AA 4 HIS A 32 MET A 38 -1 O GLN A 34 N GLY A 24
SHEET 3 AA 4 VAL A 49 HIS A 55 -1 O PHE A 50 N ILE A 37
SHEET 4 AA 4 LYS A 66 PHE A 69 -1 O LYS A 66 N HIS A 55
SHEET 1 BA 5 THR B 12 VAL B 17 0
SHEET 2 BA 5 MET B 1 LYS B 6 -1 O MET B 1 N VAL B 17
SHEET 3 BA 5 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6
SHEET 4 BA 5 GLN B 41 PHE B 45 -1 O ARG B 42 N VAL B 70
SHEET 5 BA 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45
SHEET 1 CA 3 SER C 398 ARG C 400 0
SHEET 2 CA 3 LEU C 425 VAL C 428 -1 O LEU C 426 N TYR C 399
SHEET 3 CA 3 GLU C 434 HIS C 436 -1 O PHE C 435 N ARG C 427
SHEET 1 CB 2 LEU C 412 CYS C 413 0
SHEET 2 CB 2 CYS C 418 ASP C 419 -1 O CYS C 418 N CYS C 413
SHEET 1 DA 4 CYS D 21 PRO D 25 0
SHEET 2 DA 4 HIS D 32 MET D 38 -1 O GLN D 34 N GLY D 24
SHEET 3 DA 4 VAL D 49 HIS D 55 -1 O PHE D 50 N ILE D 37
SHEET 4 DA 4 LYS D 66 PHE D 69 -1 O LYS D 66 N HIS D 55
SHEET 1 EA 5 THR E 12 VAL E 17 0
SHEET 2 EA 5 MET E 1 LYS E 6 -1 O MET E 1 N VAL E 17
SHEET 3 EA 5 THR E 66 LEU E 71 1 O LEU E 67 N LYS E 6
SHEET 4 EA 5 GLN E 41 PHE E 45 -1 O ARG E 42 N VAL E 70
SHEET 5 EA 5 LYS E 48 GLN E 49 -1 O LYS E 48 N PHE E 45
SHEET 1 FA 3 SER F 398 ARG F 400 0
SHEET 2 FA 3 LEU F 425 VAL F 428 -1 O LEU F 426 N TYR F 399
SHEET 3 FA 3 GLU F 434 HIS F 436 -1 O PHE F 435 N ARG F 427
SHEET 1 FB 2 LEU F 412 CYS F 413 0
SHEET 2 FB 2 CYS F 418 ASP F 419 -1 O CYS F 418 N CYS F 413
LINK SG CYS C 413 ZN ZN C1465 1555 1555 2.40
LINK SG CYS C 416 ZN ZN C1465 1555 1555 2.42
LINK SG CYS C 431 ZN ZN C1466 1555 1555 2.34
LINK ND1 HIS C 433 ZN ZN C1466 1555 1555 2.06
LINK ND1 HIS C 436 ZN ZN C1465 1555 1555 2.09
LINK SG CYS C 439 ZN ZN C1465 1555 1555 2.29
LINK SG CYS C 450 ZN ZN C1466 1555 1555 2.40
LINK SG CYS C 453 ZN ZN C1466 1555 1555 2.27
LINK SG CYS F 413 ZN ZN F1460 1555 1555 2.38
LINK SG CYS F 416 ZN ZN F1460 1555 1555 2.36
LINK SG CYS F 431 ZN ZN F1461 1555 1555 2.40
LINK ND1 HIS F 433 ZN ZN F1461 1555 1555 2.10
LINK ND1 HIS F 436 ZN ZN F1460 1555 1555 2.19
LINK SG CYS F 439 ZN ZN F1460 1555 1555 2.26
LINK SG CYS F 450 ZN ZN F1461 1555 1555 2.33
LINK SG CYS F 453 ZN ZN F1461 1555 1555 2.27
CISPEP 1 TYR A 60 PRO A 61 0 -8.46
CISPEP 2 TYR D 60 PRO D 61 0 -5.88
SITE 1 AC1 3 ALA A 2 LEU A 3 LYS A 4
SITE 1 AC2 2 ARG A 90 SER A 91
SITE 1 AC3 2 ASN A 81 SER A 83
SITE 1 AC4 2 ARG A 131 ASN A 135
SITE 1 AC5 4 GLU B 18 PRO B 19 SER B 20 HOH B2010
SITE 1 AC6 2 LYS B 11 THR B 12
SITE 1 AC7 3 ASN D 79 ASN D 81 SER D 83
SITE 1 AC8 1 SER D 91
SITE 1 AC9 3 ASN B 60 HOH B2035 ARG D 131
SITE 1 BC1 3 HOH D2059 ARG E 72 ARG E 74
SITE 1 BC2 4 CYS C 413 CYS C 416 HIS C 436 CYS C 439
SITE 1 BC3 4 CYS C 431 HIS C 433 CYS C 450 CYS C 453
SITE 1 BC4 4 CYS F 413 CYS F 416 HIS F 436 CYS F 439
SITE 1 BC5 4 CYS F 431 HIS F 433 CYS F 450 CYS F 453
CRYST1 139.620 139.620 70.690 90.00 90.00 90.00 P 41 21 2 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 0.007162 0.000000 0.000000 0.00000
SCALE2 0.000000 0.007162 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014146 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
