HEADER LIGASE 11-JAN-11 2Y4W TITLE SOLUTION STRUCTURE OF HUMAN UBIQUITIN CONJUGATING ENZYME TITLE 2 RAD6B COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RAD6 HOMOLOG B, UBIQUITIN CARRIER PROTEIN B, COMPND 5 UBIQUITIN-CONJUGATING ENZYME E2-17 KDA, UBIQUITIN-PROTEIN LIGASE COMPND 6 B, HR6B, HHR6B, RAD6B; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PLIS KEYWDS LIGASE, DNA DAMAGE, DNA REPAIR, UBIQUITINATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.HUANG,R.G.HIBBERT,R.N.DEJONG,D.DAS,T.K.SIXMA,R.BOELENS REVDAT 2 27-JUN-12 2Y4W 1 JRNL REMARK VERSN REVDAT 1 11-MAY-11 2Y4W 0 JRNL AUTH A.HUANG,R.G.HIBBERT,R.N.DEJONG,D.DAS,T.K.SIXMA,R.BOELENS JRNL TITL SYMMETRY AND ASYMMETRY OF THE RING-RING DIMER OF RAD18 JRNL REF J.MOL.BIOL. V. 410 424 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21549715 JRNL DOI 10.1016/J.JMB.2011.04.051 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, REMARK 3 : RICE,SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINMENT ACCORDING TO RECOORD REMARK 3 APPROACH REMARK 4 REMARK 4 2Y4W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JAN-11. REMARK 100 THE PDBE ID CODE IS EBI-46914. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310.0 REMARK 210 PH : 8.0 REMARK 210 IONIC STRENGTH : 300MM REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 50MM KH2PO4/K2HPO4 (PH 8.0), REMARK 210 300 MM NACL, 1 MM DTT, REMARK 210 95%/5% H2O/D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC, 2D 1H-13C REMARK 210 HSQC, 2D 1H-1H NOESY, 3D REMARK 210 CBCA(CO)NH, 3D C(CO)NH, 3D REMARK 210 HNCO, 3D HNCA, 3D HNCACB, REMARK 210 3D HBHA(CO)NH, 3D HN(CO)CA, REMARK 210 3D HCCH-TOCSY, 3D 1H-15N REMARK 210 NOESY, 3D 1H-13C NOESY, 3D REMARK 210 HNCACO, 3D CNH-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY REMARK 210 METHOD USED : CYANA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE REMARK 210 NMR SPECTROSCOPY ON 13C, 15N-LABELED RAD6B REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 HD21 ASN A 117 H ASN A 119 1.50 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 1 ASP A 19 84.10 -162.30 REMARK 500 1 SER A 29 -89.20 -96.76 REMARK 500 1 ASN A 32 176.58 -55.34 REMARK 500 1 GLU A 62 -83.72 -60.63 REMARK 500 1 PRO A 67 109.15 -47.02 REMARK 500 1 SER A 120 75.07 56.70 REMARK 500 1 GLU A 132 -73.46 -93.69 REMARK 500 2 SER A 2 103.84 59.65 REMARK 500 2 ASP A 19 81.42 -165.70 REMARK 500 2 SER A 29 -83.21 -86.26 REMARK 500 2 ASN A 32 -172.89 -63.31 REMARK 500 2 PRO A 47 0.09 -65.45 REMARK 500 2 GLU A 62 -77.84 -61.35 REMARK 500 2 PRO A 68 -177.27 -69.56 REMARK 500 2 ARG A 71 138.28 -171.31 REMARK 500 2 GLN A 93 -162.97 -100.89 REMARK 500 2 PRO A 118 26.36 -76.90 REMARK 500 2 GLU A 132 -78.68 -88.14 REMARK 500 3 ASP A 19 81.60 -150.23 REMARK 500 3 SER A 29 -70.34 -65.42 REMARK 500 3 GLU A 30 -39.64 -173.45 REMARK 500 3 ASN A 31 99.58 -65.98 REMARK 500 3 ASN A 32 -167.97 56.12 REMARK 500 3 PRO A 47 5.39 -68.41 REMARK 500 3 GLU A 62 -82.08 -58.48 REMARK 500 3 GLN A 93 -159.91 -76.40 REMARK 500 3 PRO A 116 -175.16 -68.74 REMARK 500 3 GLU A 132 -81.98 -82.04 REMARK 500 4 ASP A 19 86.57 -156.57 REMARK 500 4 GLU A 30 -80.61 62.86 REMARK 500 4 ASN A 32 -174.21 -59.27 REMARK 500 4 PRO A 43 -171.73 -69.63 REMARK 500 4 GLU A 61 88.02 -62.38 REMARK 500 4 GLU A 62 -79.35 -134.93 REMARK 500 4 GLN A 93 -162.54 -73.08 REMARK 500 4 PRO A 116 -174.14 -69.52 REMARK 500 4 PRO A 118 23.74 -77.77 REMARK 500 4 GLU A 132 -83.75 -102.39 REMARK 500 4 ASN A 150 90.61 56.93 REMARK 500 4 ASP A 151 -10.63 -140.83 REMARK 500 5 ASP A 19 85.18 -164.20 REMARK 500 5 SER A 29 -81.29 -88.24 REMARK 500 5 GLU A 62 -83.80 -57.51 REMARK 500 5 PRO A 68 -174.57 -65.72 REMARK 500 5 GLN A 93 -164.08 -77.29 REMARK 500 5 SER A 120 75.08 -154.27 REMARK 500 5 GLU A 132 -80.15 -101.46 REMARK 500 6 ASP A 19 85.32 -151.13 REMARK 500 6 SER A 29 -68.22 -94.56 REMARK 500 6 GLU A 30 -35.42 -133.24 REMARK 500 REMARK 500 THIS ENTRY HAS 191 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NXA RELATED DB: PDB REMARK 900 HOMOLOGY MODELED UBIQUITIN-PROTEIN LIGASE B REMARK 900 RELATED ID: 1JAS RELATED DB: PDB REMARK 900 HSUBC2B REMARK 900 RELATED ID: 2Y43 RELATED DB: PDB REMARK 900 RAD18 UBIQUITIN LIGASE RING DOMAIN STRUCTURE DBREF 2Y4W A 1 152 UNP P63146 UBE2B_HUMAN 1 152 SEQRES 1 A 152 MET SER THR PRO ALA ARG ARG ARG LEU MET ARG ASP PHE SEQRES 2 A 152 LYS ARG LEU GLN GLU ASP PRO PRO VAL GLY VAL SER GLY SEQRES 3 A 152 ALA PRO SER GLU ASN ASN ILE MET GLN TRP ASN ALA VAL SEQRES 4 A 152 ILE PHE GLY PRO GLU GLY THR PRO PHE GLU ASP GLY THR SEQRES 5 A 152 PHE LYS LEU VAL ILE GLU PHE SER GLU GLU TYR PRO ASN SEQRES 6 A 152 LYS PRO PRO THR VAL ARG PHE LEU SER LYS MET PHE HIS SEQRES 7 A 152 PRO ASN VAL TYR ALA ASP GLY SER ILE CYS LEU ASP ILE SEQRES 8 A 152 LEU GLN ASN ARG TRP SER PRO THR TYR ASP VAL SER SER SEQRES 9 A 152 ILE LEU THR SER ILE GLN SER LEU LEU ASP GLU PRO ASN SEQRES 10 A 152 PRO ASN SER PRO ALA ASN SER GLN ALA ALA GLN LEU TYR SEQRES 11 A 152 GLN GLU ASN LYS ARG GLU TYR GLU LYS ARG VAL SER ALA SEQRES 12 A 152 ILE VAL GLU GLN SER TRP ASN ASP SER HELIX 1 1 THR A 3 ASP A 19 1 17 HELIX 2 2 LEU A 89 GLN A 93 5 5 HELIX 3 3 VAL A 102 GLU A 115 1 14 HELIX 4 4 ASN A 123 ASN A 133 1 11 HELIX 5 5 ASN A 133 SER A 148 1 16 SHEET 1 AA 4 VAL A 24 ALA A 27 0 SHEET 2 AA 4 ASN A 37 PHE A 41 -1 O ASN A 37 N ALA A 27 SHEET 3 AA 4 THR A 52 GLU A 58 -1 O PHE A 53 N ILE A 40 SHEET 4 AA 4 THR A 69 PHE A 72 -1 O THR A 69 N GLU A 58 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1