PDB Short entry for 1TTE HEADER LIGASE 22-JUN-04 1TTE TITLE THE STRUCTURE OF A CLASS II UBIQUITIN-CONJUGATING ENZYME, UBC1. COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2-24 KDA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UBC1; COMPND 5 SYNONYM: UBIQUITIN-PROTEIN LIGASE, UBIQUITIN CARRIER PROTEIN; COMPND 6 EC: 6.3.2.19; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: UBC1, YDR177W, YD9395.10; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS UBC1, E2, UBIQUITIN-DEPENDENT DEGRADATION, LIGASE EXPDTA SOLUTION NMR NUMMDL 21 AUTHOR N.MERKLEY,G.S.SHAW REVDAT 4 27-OCT-21 1TTE 1 REMARK SEQADV REVDAT 3 24-FEB-09 1TTE 1 VERSN REVDAT 2 16-NOV-04 1TTE 1 JRNL REVDAT 1 31-AUG-04 1TTE 0 JRNL AUTH N.MERKLEY,G.S.SHAW JRNL TITL SOLUTION STRUCTURE OF THE FLEXIBLE CLASS II JRNL TITL 2 UBIQUITIN-CONJUGATING ENZYME UBC1 PROVIDES INSIGHTS FOR JRNL TITL 3 POLYUBIQUITIN CHAIN ASSEMBLY. JRNL REF J.BIOL.CHEM. V. 279 47139 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15328341 JRNL DOI 10.1074/JBC.M409576200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : A.T.BRUNGER, P.D.ADAMS, G.M.CLORE, W.L.DELANO, REMARK 3 P.GROS, R.W.GROSSE-KUNSTLEVE, J.-S.JIANG, REMARK 3 J.KUSZEWSKI, M.NILGES, N.S.PANNU, R.J.READ, REMARK 3 L.M.RICE, T.SIMONSON, G.L.WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TTE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000022887. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 150 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.48MM U-15N,13C UBC1; 25 MM REMARK 210 TRIS; 1 MM EDTA, 1MM REMARK 210 DITHIOTHREITOL, 150 MM NACL; REMARK 210 0.48 MM U-15N UBC1; 25 MM TRIS; REMARK 210 1 MM, 1 MM EDTA, 1MM DTT, 150 MM REMARK 210 NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, PIPP/STAPP 4.3.3, REMARK 210 VNMR 6.1C REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 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 16 78.48 -65.28 REMARK 500 1 ASP A 17 145.41 62.64 REMARK 500 1 PRO A 18 86.99 -54.99 REMARK 500 1 ALA A 20 -4.88 78.85 REMARK 500 1 GLU A 29 -164.93 -58.72 REMARK 500 1 ILE A 32 105.44 -56.83 REMARK 500 1 PRO A 43 -158.77 -72.96 REMARK 500 1 THR A 45 144.99 -177.81 REMARK 500 1 PRO A 59 -166.99 -76.38 REMARK 500 1 MET A 60 50.31 -114.22 REMARK 500 1 PHE A 64 79.58 57.45 REMARK 500 1 PHE A 71 -91.12 63.34 REMARK 500 1 ASP A 72 93.34 41.36 REMARK 500 1 THR A 73 23.38 46.22 REMARK 500 1 LYS A 74 36.19 35.47 REMARK 500 1 SER A 81 82.29 70.89 REMARK 500 1 VAL A 83 -46.25 -144.98 REMARK 500 1 THR A 84 30.80 -142.13 REMARK 500 1 ASP A 90 -83.24 56.00 REMARK 500 1 LEU A 92 -53.55 -144.61 REMARK 500 1 ASN A 94 83.97 -167.66 REMARK 500 1 SER A 97 120.23 -179.19 REMARK 500 1 ILE A 100 91.36 -55.20 REMARK 500 1 GLN A 114 31.64 -97.95 REMARK 500 1 PRO A 121 -158.72 -79.86 REMARK 500 1 SER A 153 -178.59 60.96 REMARK 500 1 LYS A 157 -57.63 -131.47 REMARK 500 1 GLU A 161 -176.10 61.10 REMARK 500 1 SER A 163 -47.77 -144.72 REMARK 500 1 ASP A 169 -85.14 -155.44 REMARK 500 1 LEU A 193 -80.19 -76.06 REMARK 500 1 ASN A 201 45.65 -140.54 REMARK 500 1 ASP A 202 58.14 -165.47 REMARK 500 1 LEU A 214 35.07 -85.82 REMARK 500 2 PRO A 18 69.99 -65.40 REMARK 500 2 ALA A 19 -66.17 -153.51 REMARK 500 2 HIS A 21 89.84 62.20 REMARK 500 2 SER A 28 -78.74 174.96 REMARK 500 2 TYR A 47 52.26 -93.42 REMARK 500 2 LYS A 51 88.11 -151.63 REMARK 500 2 PRO A 59 -156.84 -69.14 REMARK 500 2 PHE A 64 36.27 -178.01 REMARK 500 2 PRO A 66 167.49 -49.75 REMARK 500 2 LYS A 74 144.59 63.11 REMARK 500 2 SER A 81 114.28 64.75 REMARK 500 2 SER A 82 -51.39 -160.26 REMARK 500 2 VAL A 83 -45.98 -135.73 REMARK 500 2 ILE A 91 18.19 -149.85 REMARK 500 2 ASN A 94 40.25 179.41 REMARK 500 2 VAL A 99 -81.54 -121.08 REMARK 500 REMARK 500 THIS ENTRY HAS 763 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1TTE A 1 215 UNP P21734 UBC1_YEAST 1 215 SEQADV 1TTE SER A 1 UNP P21734 MET 1 ENGINEERED MUTATION SEQADV 1TTE ARG A 93 UNP P21734 LYS 93 ENGINEERED MUTATION SEQRES 1 A 215 SER SER ARG ALA LYS ARG ILE MET LYS GLU ILE GLN ALA SEQRES 2 A 215 VAL LYS ASP ASP PRO ALA ALA HIS ILE THR LEU GLU PHE SEQRES 3 A 215 VAL SER GLU SER ASP ILE HIS HIS LEU LYS GLY THR PHE SEQRES 4 A 215 LEU GLY PRO PRO GLY THR PRO TYR GLU GLY GLY LYS PHE SEQRES 5 A 215 VAL VAL ASP ILE GLU VAL PRO MET GLU TYR PRO PHE LYS SEQRES 6 A 215 PRO PRO LYS MET GLN PHE ASP THR LYS VAL TYR HIS PRO SEQRES 7 A 215 ASN ILE SER SER VAL THR GLY ALA ILE CYS LEU ASP ILE SEQRES 8 A 215 LEU ARG ASN ALA TRP SER PRO VAL ILE THR LEU LYS SER SEQRES 9 A 215 ALA LEU ILE SER LEU GLN ALA LEU LEU GLN SER PRO GLU SEQRES 10 A 215 PRO ASN ASP PRO GLN ASP ALA GLU VAL ALA GLN HIS TYR SEQRES 11 A 215 LEU ARG ASP ARG GLU SER PHE ASN LYS THR ALA ALA LEU SEQRES 12 A 215 TRP THR ARG LEU TYR ALA SER GLU THR SER ASN GLY GLN SEQRES 13 A 215 LYS GLY ASN VAL GLU GLU SER ASP LEU TYR GLY ILE ASP SEQRES 14 A 215 HIS ASP LEU ILE ASP GLU PHE GLU SER GLN GLY PHE GLU SEQRES 15 A 215 LYS ASP LYS ILE VAL GLU VAL LEU ARG ARG LEU GLY VAL SEQRES 16 A 215 LYS SER LEU ASP PRO ASN ASP ASN ASN THR ALA ASN ARG SEQRES 17 A 215 ILE ILE GLU GLU LEU LEU LYS HELIX 1 1 ARG A 3 ASP A 16 1 14 HELIX 2 2 THR A 101 GLN A 114 1 14 HELIX 3 3 ASP A 123 ASP A 133 1 11 HELIX 4 4 ASP A 133 TYR A 148 1 16 HELIX 5 5 ASP A 169 GLY A 180 1 12 HELIX 6 6 GLU A 182 LEU A 193 1 12 HELIX 7 7 ASN A 203 LEU A 214 1 12 SHEET 1 A 4 THR A 23 LEU A 24 0 SHEET 2 A 4 HIS A 34 THR A 38 -1 O THR A 38 N THR A 23 SHEET 3 A 4 VAL A 53 GLU A 57 -1 O ILE A 56 N LEU A 35 SHEET 4 A 4 LYS A 68 GLN A 70 -1 O GLN A 70 N ASP A 55 SHEET 1 B 2 GLY A 41 THR A 45 0 SHEET 2 B 2 GLU A 48 GLY A 50 -1 O GLY A 50 N GLY A 41 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