PDB Short entry for 2K07 HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 25-JAN-08 2K07 TITLE SOLUTION NMR STRUCTURE OF HUMAN E2-LIKE UBIQUITIN-FOLD MODIFIER TITLE 2 CONJUGATING ENZYME 1 (UFC1). NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TITLE 3 TARGET HR41 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UFM1-CONJUGATING ENZYME 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBIQUITIN-FOLD MODIFIER-CONJUGATING ENZYME 1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UFC1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS UFC1, UBIQUITIN CONJUGATING ENZYME, E2, UFM1, POLYMORPHISM, UBL KEYWDS 2 CONJUGATION PATHWAY, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, UNKNOWN KEYWDS 4 FUNCTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.LIU,A.ELETSKY,H.S.ATREYA,J.M.ARAMINI,R.XIAO,T.ACTON,G.T.MONTELIONE, AUTHOR 2 T.SZYPERSKI,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 4 16-MAR-22 2K07 1 REMARK SEQADV REVDAT 3 29-SEP-09 2K07 1 JRNL REVDAT 2 24-FEB-09 2K07 1 VERSN REVDAT 1 19-FEB-08 2K07 0 SPRSDE 19-FEB-08 2K07 1YWZ JRNL AUTH G.LIU,F.FOROUHAR,A.ELETSKY,H.S.ATREYA,J.M.ARAMINI,R.XIAO, JRNL AUTH 2 Y.J.HUANG,M.ABASHIDZE,J.SEETHARAMAN,J.LIU,B.ROST,T.ACTON, JRNL AUTH 3 G.T.MONTELIONE,J.F.HUNT,T.SZYPERSKI JRNL TITL NMR AND X-RAY STRUCTURES OF HUMAN E2-LIKE UBIQUITIN-FOLD JRNL TITL 2 MODIFIER CONJUGATING ENZYME 1 (UFC1) REVEAL STRUCTURAL AND JRNL TITL 3 FUNCTIONAL CONSERVATION IN THE METAZOAN UFM1-UBA5-UFC1 JRNL TITL 4 UBIQUINATION PATHWAY. JRNL REF J.STRUCT.FUNCT.GENOM. V. 10 127 2009 JRNL REFN ISSN 1345-711X JRNL PMID 19101823 JRNL DOI 10.1007/S10969-008-9054-7 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, CYANA 2.1 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), GUNTERT, MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K07 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000100510. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NA REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.1 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN UFC1, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; SIMULTANEOUS REMARK 210 HETERONUCLEAR RESOLVED [1H,1H]- REMARK 210 NOESY; GFT (4,3)D HNNCABCA; GFT REMARK 210 (4,3)D CABCA(CO)NHN; GFT (4,3)D REMARK 210 HABCAB(CO)NHN; GFT (4,3) HCCH REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, AUTOSTRUCTURE 2.2.1, REMARK 210 AUTOASSIGN 2.1, XEASY 1.3.1.3, REMARK 210 NMRPIPE 2.3, VNMR REMARK 210 METHOD USED : MOLECULAR DYNAMICS, SIMULATED REMARK 210 ANNEALING, DISTANCE GEOMETRY, REMARK 210 TORSION ANGLE DYNAMICS 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 : 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 HZ1 LYS A 164 OE1 GLU A 169 1.60 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 ALA A 2 -161.02 -102.73 REMARK 500 1 ASN A 19 81.13 46.25 REMARK 500 1 TRP A 53 -68.69 -104.94 REMARK 500 1 ASP A 74 -85.95 68.30 REMARK 500 1 PRO A 130 -120.08 -96.72 REMARK 500 1 HIS A 161 41.41 -152.24 REMARK 500 1 CYS A 165 -43.23 -137.82 REMARK 500 1 ASN A 166 95.04 59.68 REMARK 500 1 GLN A 167 -29.98 72.49 REMARK 500 1 LEU A 168 -71.00 -60.61 REMARK 500 1 GLU A 169 -75.31 -84.76 REMARK 500 1 HIS A 172 93.61 -64.68 REMARK 500 1 HIS A 173 99.07 -172.65 REMARK 500 2 PRO A 14 151.20 -45.52 REMARK 500 2 LEU A 75 -38.64 72.65 REMARK 500 2 THR A 89 40.50 -83.19 REMARK 500 2 ILE A 97 116.24 65.95 REMARK 500 2 LYS A 108 35.81 -96.19 REMARK 500 2 PRO A 130 -153.33 -89.05 REMARK 500 2 HIS A 161 95.78 -67.44 REMARK 500 3 ASP A 3 73.16 58.40 REMARK 500 3 LEU A 75 -20.03 75.36 REMARK 500 3 ASP A 103 109.64 -50.86 REMARK 500 3 LYS A 108 -29.56 75.31 REMARK 500 3 PRO A 130 -152.88 -93.36 REMARK 500 3 LYS A 131 -5.96 77.21 REMARK 500 4 LEU A 75 -0.60 70.11 REMARK 500 4 ARG A 111 82.18 -156.49 REMARK 500 4 PRO A 130 -147.55 -90.43 REMARK 500 4 LYS A 162 -158.05 -135.96 REMARK 500 5 ALA A 20 -65.50 -140.45 REMARK 500 5 ASN A 51 72.96 -118.39 REMARK 500 5 ARG A 111 84.14 -66.60 REMARK 500 5 PRO A 130 -158.25 -89.98 REMARK 500 5 CYS A 165 87.03 55.13 REMARK 500 6 TRP A 53 -78.78 -88.79 REMARK 500 6 LEU A 75 -4.89 71.92 REMARK 500 6 PRO A 130 -159.47 -84.29 REMARK 500 6 LYS A 162 -71.56 -102.25 REMARK 500 6 LYS A 164 -79.01 -99.97 REMARK 500 7 ALA A 2 -156.00 -118.30 REMARK 500 7 PRO A 22 2.39 -69.29 REMARK 500 7 PHE A 66 86.06 -152.36 REMARK 500 7 LEU A 75 -33.43 74.46 REMARK 500 7 TYR A 110 95.55 64.17 REMARK 500 7 PRO A 130 -154.70 -95.98 REMARK 500 7 CYS A 165 50.74 -95.39 REMARK 500 7 GLN A 167 135.91 -178.90 REMARK 500 8 ALA A 107 -154.80 -66.99 REMARK 500 8 GLN A 160 105.10 -59.88 REMARK 500 REMARK 500 THIS ENTRY HAS 142 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HR41 RELATED DB: TARGETDB REMARK 900 RELATED ID: 6546 RELATED DB: BMRB DBREF 2K07 A 1 167 UNP Q9Y3C8 UFC1_HUMAN 1 167 SEQADV 2K07 LEU A 168 UNP Q9Y3C8 EXPRESSION TAG SEQADV 2K07 GLU A 169 UNP Q9Y3C8 EXPRESSION TAG SEQADV 2K07 HIS A 170 UNP Q9Y3C8 EXPRESSION TAG SEQADV 2K07 HIS A 171 UNP Q9Y3C8 EXPRESSION TAG SEQADV 2K07 HIS A 172 UNP Q9Y3C8 EXPRESSION TAG SEQADV 2K07 HIS A 173 UNP Q9Y3C8 EXPRESSION TAG SEQADV 2K07 HIS A 174 UNP Q9Y3C8 EXPRESSION TAG SEQADV 2K07 HIS A 175 UNP Q9Y3C8 EXPRESSION TAG SEQRES 1 A 175 MET ALA ASP GLU ALA THR ARG ARG VAL VAL SER GLU ILE SEQRES 2 A 175 PRO VAL LEU LYS THR ASN ALA GLY PRO ARG ASP ARG GLU SEQRES 3 A 175 LEU TRP VAL GLN ARG LEU LYS GLU GLU TYR GLN SER LEU SEQRES 4 A 175 ILE ARG TYR VAL GLU ASN ASN LYS ASN ALA ASP ASN ASP SEQRES 5 A 175 TRP PHE ARG LEU GLU SER ASN LYS GLU GLY THR ARG TRP SEQRES 6 A 175 PHE GLY LYS CYS TRP TYR ILE HIS ASP LEU LEU LYS TYR SEQRES 7 A 175 GLU PHE ASP ILE GLU PHE ASP ILE PRO ILE THR TYR PRO SEQRES 8 A 175 THR THR ALA PRO GLU ILE ALA VAL PRO GLU LEU ASP GLY SEQRES 9 A 175 LYS THR ALA LYS MET TYR ARG GLY GLY LYS ILE CYS LEU SEQRES 10 A 175 THR ASP HIS PHE LYS PRO LEU TRP ALA ARG ASN VAL PRO SEQRES 11 A 175 LYS PHE GLY LEU ALA HIS LEU MET ALA LEU GLY LEU GLY SEQRES 12 A 175 PRO TRP LEU ALA VAL GLU ILE PRO ASP LEU ILE GLN LYS SEQRES 13 A 175 GLY VAL ILE GLN HIS LYS GLU LYS CYS ASN GLN LEU GLU SEQRES 14 A 175 HIS HIS HIS HIS HIS HIS HELIX 1 1 ASP A 3 GLU A 12 1 10 HELIX 2 2 ASP A 24 ALA A 49 1 26 HELIX 3 3 HIS A 120 VAL A 129 1 10 HELIX 4 4 GLY A 133 GLY A 141 1 9 HELIX 5 5 GLY A 141 LYS A 156 1 16 SHEET 1 A 3 PHE A 54 SER A 58 0 SHEET 2 A 3 ARG A 64 HIS A 73 -1 O PHE A 66 N GLU A 57 SHEET 3 A 3 LEU A 76 ASP A 85 -1 O PHE A 80 N CYS A 69 CISPEP 1 TYR A 90 PRO A 91 1 3.72 CISPEP 2 VAL A 129 PRO A 130 1 2.67 CISPEP 3 TYR A 90 PRO A 91 2 -2.23 CISPEP 4 VAL A 129 PRO A 130 2 1.02 CISPEP 5 TYR A 90 PRO A 91 3 0.16 CISPEP 6 VAL A 129 PRO A 130 3 2.21 CISPEP 7 TYR A 90 PRO A 91 4 -1.25 CISPEP 8 VAL A 129 PRO A 130 4 5.78 CISPEP 9 TYR A 90 PRO A 91 5 2.13 CISPEP 10 VAL A 129 PRO A 130 5 -0.20 CISPEP 11 TYR A 90 PRO A 91 6 1.12 CISPEP 12 VAL A 129 PRO A 130 6 6.49 CISPEP 13 TYR A 90 PRO A 91 7 0.59 CISPEP 14 VAL A 129 PRO A 130 7 1.87 CISPEP 15 TYR A 90 PRO A 91 8 -0.13 CISPEP 16 VAL A 129 PRO A 130 8 3.88 CISPEP 17 TYR A 90 PRO A 91 9 1.53 CISPEP 18 VAL A 129 PRO A 130 9 1.03 CISPEP 19 TYR A 90 PRO A 91 10 -2.68 CISPEP 20 VAL A 129 PRO A 130 10 7.17 CISPEP 21 TYR A 90 PRO A 91 11 1.06 CISPEP 22 VAL A 129 PRO A 130 11 4.14 CISPEP 23 TYR A 90 PRO A 91 12 0.37 CISPEP 24 VAL A 129 PRO A 130 12 0.19 CISPEP 25 TYR A 90 PRO A 91 13 -0.10 CISPEP 26 VAL A 129 PRO A 130 13 3.11 CISPEP 27 TYR A 90 PRO A 91 14 -1.33 CISPEP 28 VAL A 129 PRO A 130 14 5.13 CISPEP 29 TYR A 90 PRO A 91 15 1.83 CISPEP 30 VAL A 129 PRO A 130 15 1.69 CISPEP 31 TYR A 90 PRO A 91 16 0.64 CISPEP 32 VAL A 129 PRO A 130 16 2.09 CISPEP 33 TYR A 90 PRO A 91 17 2.71 CISPEP 34 VAL A 129 PRO A 130 17 4.53 CISPEP 35 TYR A 90 PRO A 91 18 -1.13 CISPEP 36 VAL A 129 PRO A 130 18 5.87 CISPEP 37 TYR A 90 PRO A 91 19 2.54 CISPEP 38 VAL A 129 PRO A 130 19 4.23 CISPEP 39 TYR A 90 PRO A 91 20 1.15 CISPEP 40 VAL A 129 PRO A 130 20 6.45 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