HEADER PROTEIN BINDING 29-MAY-04 1WJU TITLE SOLUTION STRUCTURE OF N-TERMINAL UBIQUITIN-LIKE DOMAIN OF HUMAN NEDD8 TITLE 2 ULTIMATE BUSTER-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEDD8 ULTIMATE BUSTER-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UBIQUITIN-LIKE DOMAIN; COMPND 5 SYNONYM: NY-REN-18 ANTIGEN; COMPND 6 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: IMS CDNA SYN05355; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P040301-74; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS UBIQUITIN-LIKE DOMAIN, NEDD8 ULTIMATE BUSTER-1, STRUCTURAL GENOMICS, KEYWDS 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, PROTEIN KEYWDS 3 BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.YONEYAMA,S.KOSHIBA,N.TOCHIO,M.INOUE,T.KIGAWA,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 02-MAR-22 1WJU 1 REMARK SEQADV REVDAT 3 24-FEB-09 1WJU 1 VERSN REVDAT 2 17-JAN-06 1WJU 1 TITLE JRNL REVDAT 1 29-NOV-04 1WJU 0 JRNL AUTH M.YONEYAMA,S.KOSHIBA,N.TOCHIO,M.INOUE,T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF N-TERMINAL UBIQUITIN-LIKE DOMAIN OF JRNL TITL 2 HUMAN NEDD8 ULTIMATE BUSTER-1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 20020425, CYANA 1.0.8 REMARK 3 AUTHORS : DELAGLIO, F. (NMRPIPE), GUENTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WJU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000023654. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM UBIQUITIN-LIKE DOMAIN U-15N, REMARK 210 13C; 20MM D-TRIS-HCL; 100MM NACL; REMARK 210 1MM D-DTT; 0.02% NAN3; 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW 5.0.4, KUJIRA 0.896, REMARK 210 CYANA 1.0.8, XWINNMR 3.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, TARGET REMARK 210 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 O LYS A 48 H THR A 52 1.48 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 SER A 2 141.29 62.89 REMARK 500 1 SER A 6 162.86 66.66 REMARK 500 1 ASN A 9 -51.41 -147.67 REMARK 500 1 ARG A 11 137.33 178.96 REMARK 500 1 ARG A 25 -47.10 -134.15 REMARK 500 1 LYS A 27 100.93 53.08 REMARK 500 1 ARG A 30 -173.49 -54.30 REMARK 500 1 ALA A 50 -70.51 -49.02 REMARK 500 1 LYS A 66 28.04 43.21 REMARK 500 1 ALA A 81 -166.51 -107.64 REMARK 500 2 SER A 2 142.97 66.16 REMARK 500 2 ASN A 9 -55.87 -178.29 REMARK 500 2 TYR A 10 98.53 49.92 REMARK 500 2 ARG A 11 159.13 178.12 REMARK 500 2 THR A 12 87.17 40.26 REMARK 500 2 LEU A 26 -75.62 -121.30 REMARK 500 2 LYS A 27 83.95 71.39 REMARK 500 2 ALA A 50 -70.98 -40.28 REMARK 500 2 LYS A 66 27.08 46.60 REMARK 500 2 ASN A 83 73.87 70.23 REMARK 500 2 LEU A 91 170.86 -53.63 REMARK 500 2 GLN A 93 85.12 -178.36 REMARK 500 2 SER A 95 164.96 63.78 REMARK 500 2 SER A 98 155.28 65.05 REMARK 500 2 SER A 99 92.34 62.07 REMARK 500 3 SER A 2 164.45 176.31 REMARK 500 3 SER A 3 -59.29 80.15 REMARK 500 3 SER A 5 113.67 -173.64 REMARK 500 3 ASP A 8 -71.64 67.79 REMARK 500 3 ASN A 9 122.97 61.86 REMARK 500 3 ARG A 25 -44.34 -132.16 REMARK 500 3 LYS A 27 96.82 49.34 REMARK 500 3 ASP A 29 121.52 71.75 REMARK 500 3 LYS A 31 82.65 -179.19 REMARK 500 3 LYS A 48 -70.05 -60.66 REMARK 500 3 ALA A 50 -70.65 -57.17 REMARK 500 3 ALA A 81 -100.14 -111.90 REMARK 500 3 SER A 95 100.81 55.62 REMARK 500 3 SER A 98 170.37 65.48 REMARK 500 3 SER A 99 -58.71 -129.53 REMARK 500 4 SER A 5 86.05 -155.96 REMARK 500 4 SER A 6 81.40 176.39 REMARK 500 4 ASP A 8 120.32 -171.24 REMARK 500 4 ARG A 11 115.23 -160.09 REMARK 500 4 THR A 12 86.59 -63.20 REMARK 500 4 ARG A 25 -31.38 168.70 REMARK 500 4 LEU A 26 -67.74 -103.26 REMARK 500 4 LYS A 27 90.89 42.13 REMARK 500 4 ARG A 30 173.25 54.49 REMARK 500 4 LYS A 31 177.61 -51.53 REMARK 500 REMARK 500 THIS ENTRY HAS 294 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSS001003749.1 RELATED DB: TARGETDB DBREF 1WJU A 8 94 UNP Q9Y5A7 NUB1_HUMAN 75 161 SEQADV 1WJU GLY A 1 UNP Q9Y5A7 CLONING ARTIFACT SEQADV 1WJU SER A 2 UNP Q9Y5A7 CLONING ARTIFACT SEQADV 1WJU SER A 3 UNP Q9Y5A7 CLONING ARTIFACT SEQADV 1WJU GLY A 4 UNP Q9Y5A7 CLONING ARTIFACT SEQADV 1WJU SER A 5 UNP Q9Y5A7 CLONING ARTIFACT SEQADV 1WJU SER A 6 UNP Q9Y5A7 CLONING ARTIFACT SEQADV 1WJU GLY A 7 UNP Q9Y5A7 CLONING ARTIFACT SEQADV 1WJU SER A 95 UNP Q9Y5A7 CLONING ARTIFACT SEQADV 1WJU GLY A 96 UNP Q9Y5A7 CLONING ARTIFACT SEQADV 1WJU PRO A 97 UNP Q9Y5A7 CLONING ARTIFACT SEQADV 1WJU SER A 98 UNP Q9Y5A7 CLONING ARTIFACT SEQADV 1WJU SER A 99 UNP Q9Y5A7 CLONING ARTIFACT SEQADV 1WJU GLY A 100 UNP Q9Y5A7 CLONING ARTIFACT SEQRES 1 A 100 GLY SER SER GLY SER SER GLY ASP ASN TYR ARG THR THR SEQRES 2 A 100 GLY ILE ALA THR ILE GLU VAL PHE LEU PRO PRO ARG LEU SEQRES 3 A 100 LYS LYS ASP ARG LYS ASN LEU LEU GLU THR ARG LEU HIS SEQRES 4 A 100 ILE THR GLY ARG GLU LEU ARG SER LYS ILE ALA GLU THR SEQRES 5 A 100 PHE GLY LEU GLN GLU ASN TYR ILE LYS ILE VAL ILE ASN SEQRES 6 A 100 LYS LYS GLN LEU GLN LEU GLY LYS THR LEU GLU GLU GLN SEQRES 7 A 100 GLY VAL ALA HIS ASN VAL LYS ALA MET VAL LEU GLU LEU SEQRES 8 A 100 LYS GLN SER SER GLY PRO SER SER GLY HELIX 1 1 THR A 41 PHE A 53 1 13 HELIX 2 2 THR A 74 GLY A 79 1 6 SHEET 1 A 5 ASN A 32 ARG A 37 0 SHEET 2 A 5 ILE A 15 PHE A 21 -1 N ILE A 18 O LEU A 34 SHEET 3 A 5 VAL A 84 LEU A 89 1 O ALA A 86 N GLU A 19 SHEET 4 A 5 LYS A 61 ILE A 64 -1 N VAL A 63 O MET A 87 SHEET 5 A 5 LYS A 67 GLN A 68 -1 O LYS A 67 N ILE A 64 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