PDB Short entry for 2MWS HEADER PROTEIN TRANSPORT 23-NOV-14 2MWS TITLE STRUCTURE OF THE COMPLEX OF UBIQUITIN AND THE UBIQUITIN-LIKE (UBL) TITLE 2 DOMAIN OF DDI1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-76; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA DAMAGE-INDUCIBLE PROTEIN 1; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 2-80; COMPND 11 SYNONYM: V-SNARE-MASTER 1; COMPND 12 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: UBC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET3A; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 11 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 12 ORGANISM_TAXID: 559292; SOURCE 13 STRAIN: ATCC 204508 / S288C; SOURCE 14 GENE: DDI1, VSM1, YER143W; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_VECTOR: PQE30 KEYWDS UBL, DDI1, UBIQUITIN, PROTEASOME, PROTEIN TRANSPORT EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR D.FUSHMAN,U.NOWICKA,O.WALKER REVDAT 2 14-JUN-23 2MWS 1 REMARK SEQADV LINK REVDAT 1 25-MAR-15 2MWS 0 JRNL AUTH U.NOWICKA,D.ZHANG,O.WALKER,D.KRUTAUZ,C.A.CASTANEDA, JRNL AUTH 2 A.CHATURVEDI,T.Y.CHEN,N.REIS,M.H.GLICKMAN,D.FUSHMAN JRNL TITL DNA-DAMAGE-INDUCIBLE 1 PROTEIN (DDI1) CONTAINS AN JRNL TITL 2 UNCHARACTERISTIC UBIQUITIN-LIKE DOMAIN THAT BINDS UBIQUITIN. JRNL REF STRUCTURE V. 23 542 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 25703377 JRNL DOI 10.1016/J.STR.2015.01.010 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK, HADDOCK REMARK 3 AUTHORS : ALEXANDRE BONVIN (HADDOCK), ALEXANDRE BONVIN REMARK 3 (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MWS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000104141. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.002 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 250 UM CHAIN A, 250 UM [U-100% REMARK 210 15N] CHAIN B, 5 % D2O, 20 MM REMARK 210 SODIUM PHOSPHATE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 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: MTSL 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 1-8 REMARK 465 RES C SSSEQI REMARK 465 MET B -10 REMARK 465 ARG B -9 REMARK 465 GLY B -8 REMARK 465 SER B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 GLY B 0 REMARK 465 SER B 1 REMARK 465 LYS B 81 REMARK 465 LEU B 82 REMARK 465 ASN B 83 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 HZ2 LYS A 27 OD1 ASP A 52 1.57 REMARK 500 HZ2 LYS B 66 OD1 ASP B 68 1.58 REMARK 500 HZ2 LYS A 6 OD2 ASP B 68 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 GLN A 62 -167.05 -105.91 REMARK 500 1 ALA B 34 -63.42 -91.44 REMARK 500 1 ASN B 48 -78.81 67.22 REMARK 500 1 MET B 49 18.24 -145.56 REMARK 500 1 LYS B 66 -155.68 -141.52 REMARK 500 1 LYS B 76 -99.21 69.02 REMARK 500 1 ILE B 77 -80.33 -121.08 REMARK 500 1 ASN B 79 -45.58 -178.50 REMARK 500 2 GLN A 62 -167.93 -108.58 REMARK 500 2 ARG A 72 105.84 -164.17 REMARK 500 2 ASN B 48 -83.32 62.14 REMARK 500 2 MET B 49 17.16 -149.91 REMARK 500 2 LYS B 76 -100.88 73.43 REMARK 500 2 ILE B 77 -81.98 -115.05 REMARK 500 2 ASN B 79 -66.70 -169.28 REMARK 500 3 GLN A 62 -160.22 -111.87 REMARK 500 3 LYS B 42 34.05 -164.45 REMARK 500 3 ASN B 48 -83.15 64.43 REMARK 500 3 LYS B 66 -76.14 -127.85 REMARK 500 3 THR B 67 -24.15 -161.29 REMARK 500 3 LYS B 76 -163.38 67.71 REMARK 500 3 ASN B 79 -70.56 178.28 REMARK 500 4 GLN A 62 -163.13 -110.35 REMARK 500 4 ARG A 72 65.38 -172.24 REMARK 500 4 ALA B 34 -63.02 -90.49 REMARK 500 4 ASN B 48 -78.07 65.16 REMARK 500 4 MET B 49 21.21 -148.97 REMARK 500 4 ARG B 56 46.12 -96.73 REMARK 500 4 THR B 57 40.13 -79.97 REMARK 500 4 LYS B 66 -67.70 -157.79 REMARK 500 4 THR B 67 -45.95 -158.48 REMARK 500 4 ASP B 68 34.18 -89.59 REMARK 500 4 ARG B 74 -159.49 -139.35 REMARK 500 4 LYS B 76 -102.78 71.47 REMARK 500 4 ILE B 77 -58.41 -129.86 REMARK 500 4 ASN B 79 -58.29 -165.68 REMARK 500 5 GLN A 62 -165.69 -113.48 REMARK 500 5 THR B 41 -66.42 -109.01 REMARK 500 5 LYS B 42 51.52 -110.66 REMARK 500 5 ASN B 48 -77.14 65.13 REMARK 500 5 THR B 57 31.90 -84.53 REMARK 500 5 ARG B 74 -158.44 -138.75 REMARK 500 5 LYS B 76 -101.39 71.06 REMARK 500 5 ILE B 77 -73.08 -124.67 REMARK 500 5 ASN B 79 -66.77 -168.41 REMARK 500 6 ARG A 72 78.87 -109.55 REMARK 500 6 LEU B 9 -66.28 -101.65 REMARK 500 6 LYS B 42 45.02 -140.24 REMARK 500 6 ASN B 48 -82.36 63.62 REMARK 500 6 LYS B 66 -55.85 -138.07 REMARK 500 REMARK 500 THIS ENTRY HAS 71 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25088 RELATED DB: BMRB DBREF 2MWS A 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 2MWS B 2 80 UNP P40087 DDI1_YEAST 2 80 SEQADV 2MWS 3X9 A 12 UNP P0CG48 THR 12 ENGINEERED MUTATION SEQADV 2MWS MET B -10 UNP P40087 EXPRESSION TAG SEQADV 2MWS ARG B -9 UNP P40087 EXPRESSION TAG SEQADV 2MWS GLY B -8 UNP P40087 EXPRESSION TAG SEQADV 2MWS SER B -7 UNP P40087 EXPRESSION TAG SEQADV 2MWS HIS B -6 UNP P40087 EXPRESSION TAG SEQADV 2MWS HIS B -5 UNP P40087 EXPRESSION TAG SEQADV 2MWS HIS B -4 UNP P40087 EXPRESSION TAG SEQADV 2MWS HIS B -3 UNP P40087 EXPRESSION TAG SEQADV 2MWS HIS B -2 UNP P40087 EXPRESSION TAG SEQADV 2MWS HIS B -1 UNP P40087 EXPRESSION TAG SEQADV 2MWS GLY B 0 UNP P40087 EXPRESSION TAG SEQADV 2MWS SER B 1 UNP P40087 EXPRESSION TAG SEQADV 2MWS LYS B 81 UNP P40087 EXPRESSION TAG SEQADV 2MWS LEU B 82 UNP P40087 EXPRESSION TAG SEQADV 2MWS ASN B 83 UNP P40087 EXPRESSION TAG SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS 3X9 ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 B 94 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER ASP SEQRES 2 B 94 LEU THR ILE SER ASN GLU LEU THR GLY GLU ILE TYR GLY SEQRES 3 B 94 PRO ILE GLU VAL SER GLU ASP MET ALA LEU THR ASP LEU SEQRES 4 B 94 ILE ALA LEU LEU GLN ALA ASP CYS GLY PHE ASP LYS THR SEQRES 5 B 94 LYS HIS ASP LEU TYR TYR ASN MET ASP ILE LEU ASP SER SEQRES 6 B 94 ASN ARG THR GLN SER LEU LYS GLU LEU GLY LEU LYS THR SEQRES 7 B 94 ASP ASP LEU LEU LEU ILE ARG GLY LYS ILE SER ASN SER SEQRES 8 B 94 LYS LEU ASN MODRES 2MWS 3X9 A 12 CYS HET 3X9 A 12 23 HETNAM 3X9 3-{[(1-HYDROXY-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H- HETNAM 2 3X9 PYRROL-3-YL)METHYL]DISULFANYL}-L-ALANINE HETSYN 3X9 CYS WITH MTSL FORMUL 1 3X9 C12 H22 N2 O3 S2 HELIX 1 1 THR A 22 GLY A 35 1 14 HELIX 2 2 PRO A 37 ASP A 39 5 3 HELIX 3 3 LEU A 56 ASN A 60 5 5 HELIX 4 1 LEU B 25 ALA B 34 1 10 HELIX 5 2 LYS B 40 LYS B 42 5 3 HELIX 6 3 LEU B 60 LEU B 63 1 4 SHEET 1 A 5 3X9 A 12 GLU A 16 0 SHEET 2 A 5 GLN A 2 THR A 7 -1 N VAL A 5 O ILE A 13 SHEET 3 A 5 THR A 66 LEU A 71 1 O LEU A 67 N PHE A 4 SHEET 4 A 5 GLN A 41 PHE A 45 -1 N ARG A 42 O VAL A 70 SHEET 5 A 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 SHEET 1 B 5 GLU B 12 PRO B 16 0 SHEET 2 B 5 LEU B 3 ASN B 7 -1 N ILE B 5 O TYR B 14 SHEET 3 B 5 LEU B 70 ARG B 74 1 O ILE B 73 N SER B 6 SHEET 4 B 5 ASP B 44 TYR B 47 -1 N ASP B 44 O ARG B 74 SHEET 5 B 5 ASP B 50 ILE B 51 -1 O ASP B 50 N TYR B 47 LINK C LYS A 11 N 3X9 A 12 1555 1555 1.33 LINK C 3X9 A 12 N ILE A 13 1555 1555 1.32 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