HEADER PROTEIN BINDING 05-OCT-10 2L4F TITLE NMR STRUCTURE OF THE UBA DOMAIN OF S. CEREVISIAE DCN1 BOUND TO TITLE 2 UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEFECTIVE IN CULLIN NEDDYLATION PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UBA DOMAIN (UNP RESIDUES 6-62); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BREWER'S YEAST,LAGER BEER YEAST,YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: DCN1, DCN1 YLR128W, L3111, YLR128W; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 STAR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-4T KEYWDS UBA, UBIQUITIN BINDING, NEDDYLATION, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.BURSCHOWSKY,D.MATTLE,F.RUDOLF,M.PETER,G.WIDER REVDAT 4 15-MAY-24 2L4F 1 REMARK REVDAT 3 14-JUN-23 2L4F 1 REMARK REVDAT 2 05-FEB-20 2L4F 1 REMARK SEQADV REVDAT 1 05-OCT-11 2L4F 0 JRNL AUTH D.BURSCHOWSKY,F.RUDOLF,D.MATTLE,M.PETER,G.WIDER JRNL TITL STRUCTURAL ANALYSIS OF THE UBIQUITIN-ASSOCIATED DOMAIN (UBA) JRNL TITL 2 OF YEAST DCN1 IN COMPLEX WITH UBIQUITIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : UNIO08 1.0.4, AMBER 9 REMARK 3 AUTHORS : HERRMANN (UNIO08), CASE, DARDEN, CHEATHAM, III, REMARK 3 SIMMERLING, WANG, DUKE, LUO, ... AND KOLLM (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L4F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000101943. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 6.15 REMARK 210 IONIC STRENGTH : 182 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-80% 13C; U-90% 15N] REMARK 210 DCN1-UBA, 15 MM SODIUM CHLORIDE, REMARK 210 110 MM POTASSIUM PHOSPHATE, 2 MM REMARK 210 DTT, 2 MM CHAPS, 0.02 % SODIUM REMARK 210 AZIDE, 25 MM SODIUM CHLORIDE, REMARK 210 3.2 MM UBIQUITIN, 95% H2O/5% D2O; REMARK 210 0.5 MM [U-90% 15N] DCN1-UBA, 15 REMARK 210 MM SODIUM PHOSPHATE, 110 MM REMARK 210 POTASSIUM PHOSPHATE, 2 MM DTT, 2 REMARK 210 MM CHAPS, 0.02 % SODIUM AZIDE, REMARK 210 25 MM SODIUM CHLORIDE, 2 MM REMARK 210 UBIQUITIN, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HCCH-COSY; 3D HNCA; 3D 1H-13C REMARK 210 NOESY; 3D 1H-13CARO NOESY; 3D 1H- REMARK 210 15N TOCSY; 3D HNHB; 3D 1H-15N REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 750 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : UNIO08 1.0.4, CYANA 2, TOPSPIN REMARK 210 2.0, CARA 1.8.4 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: UBIQUITIN PRESENT IN THE SAMPLES WAS UNLABELED 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 4 REMARK 465 SER A 5 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 LYS A 9 18.78 52.26 REMARK 500 1 ASP A 10 -38.75 -158.57 REMARK 500 1 ASN A 39 36.29 -141.23 REMARK 500 1 THR A 59 32.44 -74.37 REMARK 500 2 LYS A 9 45.15 -72.39 REMARK 500 2 ASP A 10 -38.96 -143.50 REMARK 500 2 ALA A 11 77.99 -171.50 REMARK 500 2 SER A 12 -178.82 -60.58 REMARK 500 2 ASN A 39 34.47 -141.03 REMARK 500 2 THR A 57 25.64 -144.65 REMARK 500 3 ARG A 8 35.82 -80.79 REMARK 500 3 LYS A 9 25.44 -146.03 REMARK 500 3 SER A 12 -179.23 -52.23 REMARK 500 3 ASN A 39 33.74 -140.28 REMARK 500 3 THR A 57 27.17 -141.27 REMARK 500 4 LYS A 7 50.41 -106.79 REMARK 500 4 ARG A 8 24.99 -71.58 REMARK 500 4 SER A 12 179.24 -52.58 REMARK 500 4 ASN A 39 30.38 -140.17 REMARK 500 4 THR A 57 33.39 -149.23 REMARK 500 4 THR A 59 29.04 -152.66 REMARK 500 5 LYS A 7 51.26 -105.88 REMARK 500 5 ARG A 8 28.86 -70.84 REMARK 500 5 ALA A 11 76.80 43.90 REMARK 500 5 SER A 12 163.44 -38.65 REMARK 500 5 PRO A 29 -7.91 -58.31 REMARK 500 5 ASN A 39 41.70 -145.43 REMARK 500 5 THR A 59 25.04 -79.82 REMARK 500 6 LYS A 7 46.11 -98.59 REMARK 500 6 ARG A 8 28.61 -73.51 REMARK 500 6 ASP A 10 -40.88 -148.18 REMARK 500 6 THR A 59 31.74 -86.84 REMARK 500 7 ASP A 10 -36.29 -152.82 REMARK 500 7 ALA A 11 81.66 -168.31 REMARK 500 7 SER A 12 -179.32 -59.28 REMARK 500 7 THR A 59 29.11 -75.36 REMARK 500 8 LYS A 9 12.07 -145.76 REMARK 500 8 ASP A 10 -30.27 -156.41 REMARK 500 8 ALA A 11 -128.08 53.63 REMARK 500 8 ASN A 39 37.56 -146.88 REMARK 500 8 ILE A 55 0.01 58.41 REMARK 500 8 THR A 59 30.65 -74.44 REMARK 500 9 ARG A 8 33.35 26.73 REMARK 500 9 ASP A 10 -27.21 -152.02 REMARK 500 9 ALA A 11 81.50 -163.25 REMARK 500 9 SER A 12 -178.95 -59.43 REMARK 500 9 ASN A 39 33.62 -140.98 REMARK 500 9 THR A 57 27.24 -140.58 REMARK 500 9 PHE A 58 -37.72 -145.84 REMARK 500 10 LYS A 9 44.96 -76.47 REMARK 500 REMARK 500 THIS ENTRY HAS 102 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BQ3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FULL-LENGTH DCN1 REMARK 900 RELATED ID: 17239 RELATED DB: BMRB REMARK 900 RELATED ID: 2L4E RELATED DB: PDB DBREF 2L4F A 6 62 UNP Q12395 DCN1_YEAST 6 62 SEQADV 2L4F GLY A 4 UNP Q12395 EXPRESSION TAG SEQADV 2L4F SER A 5 UNP Q12395 EXPRESSION TAG SEQRES 1 A 59 GLY SER ILE LYS ARG LYS ASP ALA SER PRO GLU GLN GLU SEQRES 2 A 59 ALA ILE GLU SER PHE THR SER LEU THR LYS CYS ASP PRO SEQRES 3 A 59 LYS VAL SER ARG LYS TYR LEU GLN ARG ASN HIS TRP ASN SEQRES 4 A 59 ILE ASN TYR ALA LEU ASN ASP TYR TYR ASP LYS GLU ILE SEQRES 5 A 59 GLY THR PHE THR ASP GLU VAL HELIX 1 1 GLU A 14 THR A 25 1 12 HELIX 2 2 ASP A 28 GLN A 37 1 10 HELIX 3 3 ASN A 42 TYR A 51 1 10 HELIX 4 4 PHE A 58 VAL A 62 5 5 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