HEADER PROTEIN BINDING 14-FEB-06 2DEN TITLE SOLUTION STRUCTURE OF THE UBIQUITIN-ASSOCIATED DOMAIN OF HUMAN BMSC- TITLE 2 UBP AND ITS COMPLEX WITH UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN G-BINDING PROTEIN G,UBIQUITIN-LIKE PROTEIN COMPND 3 7; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UBA DOMAIN,UBA DOMAIN; COMPND 6 SYNONYM: IGG-BINDING PROTEIN G,BONE MARROW STROMAL CELL UBIQUITIN- COMPND 7 LIKE PROTEIN,BMSC-UBP,UBIQUITIN-LIKE PROTEIN SB132; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 OTHER_DETAILS: HGB1-UBA IS A CHIMERIC PROTEIN. THE N-TERMINAL HISTAG COMPND 11 IS FOR EASE OF PURIFICATION. THE GB1 DOMAIN IS USED FOR SOLUBILITY COMPND 12 ENHANCEMENT. THE GB1 DOMAIN SEQUENCE REFERS TO THE PROTEIN WITH COMPND 13 ACCESSION CODE P06654.,HGB1-UBA IS A CHIMERIC PROTEIN. THE N-TERMINAL COMPND 14 HISTAG IS FOR EASE OF PURIFICATION. THE GB1 DOMAIN IS USED FOR COMPND 15 SOLUBILITY ENHANCEMENT. THE GB1 DOMAIN SEQUENCE REFERS TO THE PROTEIN COMPND 16 WITH ACCESSION CODE P06654.; COMPND 17 MOL_ID: 2; COMPND 18 MOLECULE: POLYUBIQUITIN-B; COMPND 19 CHAIN: B; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS SP. GROUP G, HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 1320, 9606; SOURCE 5 GENE: SPG, UBL7, BMSCUBP, SB132; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODONPLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHGB; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: UBB; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET-3A KEYWDS A:ALPHA-ALPHA-ALPHA, B:BETA-BETA-HELIX-HELIX-BETA-BETA-HELIX-BETA, KEYWDS 2 PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR H.Y.HU,D.H.LIN,Y.G.CHANG REVDAT 4 01-MAY-24 2DEN 1 REMARK REVDAT 3 15-JAN-20 2DEN 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 SEQADV REVDAT 2 24-FEB-09 2DEN 1 VERSN REVDAT 1 13-JUN-06 2DEN 0 JRNL AUTH Y.G.CHANG,A.X.SONG,Y.G.GAO,Y.H.SHI,X.J.LIN,X.T.CAO,D.H.LIN, JRNL AUTH 2 H.Y.HU JRNL TITL SOLUTION STRUCTURE OF THE UBIQUITIN-ASSOCIATED DOMAIN OF JRNL TITL 2 HUMAN BMSC-UBP AND ITS COMPLEX WITH UBIQUITIN JRNL REF PROTEIN SCI. V. 15 1248 2006 JRNL REFN ISSN 0961-8368 JRNL PMID 16731964 JRNL DOI 10.1110/PS.051995006 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK 1.3 REMARK 3 AUTHORS : CYRIL DOMINGUEZ, ROLF BOELENS AND ALEXANDRE M.J.J. REMARK 3 BONVIN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BASED ON NMR TITRATION DATA, THE REMARK 3 COMPLEX STRUCTRUE IS CONSTRUCTED USING THE HADDOCK PROGRAM. REMARK 4 REMARK 4 2DEN COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1000025327. 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 : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM HGB1-UBA; 1MM UBIQUITIN REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : TITRATION OF SAMPLE 1 WITH REMARK 210 SAMPLE 2; TITRATION OF SAMPLE 2 REMARK 210 WITH SAMPLE 1 REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : HADDOCK 1.3 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: THIS COMPLEX MODEL IS CONSTRUCTED BY USING THE HADDOCK REMARK 210 PROGRAM WHICH EMPLOYS THE AMBIGUOUS INTERACTION RESTRAINTS (AIR) REMARK 210 THAT ARE OBTAINED FROM THE RECIPROCAL NMR TITRATION OF THE TWO REMARK 210 SAMPLES. 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 1-10 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 HIS A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 GLN A 8 REMARK 465 TYR A 9 REMARK 465 LYS A 10 REMARK 465 LEU A 11 REMARK 465 ALA A 12 REMARK 465 LEU A 13 REMARK 465 ASN A 14 REMARK 465 GLY A 15 REMARK 465 LYS A 16 REMARK 465 THR A 17 REMARK 465 LEU A 18 REMARK 465 LYS A 19 REMARK 465 GLY A 20 REMARK 465 GLU A 21 REMARK 465 THR A 22 REMARK 465 THR A 23 REMARK 465 THR A 24 REMARK 465 GLU A 25 REMARK 465 ALA A 26 REMARK 465 VAL A 27 REMARK 465 ASP A 28 REMARK 465 ALA A 29 REMARK 465 ALA A 30 REMARK 465 THR A 31 REMARK 465 ALA A 32 REMARK 465 GLU A 33 REMARK 465 LYS A 34 REMARK 465 VAL A 35 REMARK 465 PHE A 36 REMARK 465 LYS A 37 REMARK 465 GLN A 38 REMARK 465 TYR A 39 REMARK 465 ALA A 40 REMARK 465 ASN A 41 REMARK 465 ASP A 42 REMARK 465 ASN A 43 REMARK 465 GLY A 44 REMARK 465 VAL A 45 REMARK 465 ASP A 46 REMARK 465 GLY A 47 REMARK 465 GLU A 48 REMARK 465 TRP A 49 REMARK 465 THR A 50 REMARK 465 TYR A 51 REMARK 465 ASP A 52 REMARK 465 ASP A 53 REMARK 465 ALA A 54 REMARK 465 THR A 55 REMARK 465 LYS A 56 REMARK 465 THR A 57 REMARK 465 PHE A 58 REMARK 465 THR A 59 REMARK 465 VAL A 60 REMARK 465 THR A 61 REMARK 465 GLU A 62 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 2 PHE B 45 71.06 -110.16 REMARK 500 2 ALA B 46 79.24 58.00 REMARK 500 3 THR B 7 -90.17 -68.87 REMARK 500 3 LEU B 8 -65.15 -143.64 REMARK 500 3 LYS B 11 107.33 -57.08 REMARK 500 3 GLN B 62 -166.05 -101.26 REMARK 500 4 THR B 7 -89.11 -64.76 REMARK 500 4 LEU B 8 -66.71 -141.14 REMARK 500 4 PHE B 45 75.65 -119.02 REMARK 500 5 THR B 7 -112.30 -77.82 REMARK 500 5 THR B 9 -95.84 -114.91 REMARK 500 5 LYS B 11 107.24 -58.45 REMARK 500 6 GLN A 65 -77.48 -88.14 REMARK 500 7 GLN A 65 -72.97 -81.83 REMARK 500 7 ALA B 46 -79.68 67.11 REMARK 500 8 GLN A 65 -66.37 -90.33 REMARK 500 8 ILE A 95 -62.69 -90.04 REMARK 500 8 ARG B 42 79.90 -102.18 REMARK 500 8 PHE B 45 70.01 -105.66 REMARK 500 10 ILE A 95 -65.13 -97.88 REMARK 500 10 ALA B 46 -67.12 69.46 REMARK 500 10 ARG B 74 79.77 -106.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CWB RELATED DB: PDB REMARK 900 RELATED ID: 1UBQ RELATED DB: PDB DBREF 2DEN A 9 62 UNP P06654 SPG1_STRSG 229 282 DBREF 2DEN A 64 108 UNP Q96S82 UBL7_HUMAN 336 380 DBREF 2DEN B 1 76 UNP J3QS39 J3QS39_HUMAN 1 76 SEQADV 2DEN MET A 1 UNP P06654 EXPRESSION TAG SEQADV 2DEN HIS A 2 UNP P06654 EXPRESSION TAG SEQADV 2DEN HIS A 3 UNP P06654 EXPRESSION TAG SEQADV 2DEN HIS A 4 UNP P06654 EXPRESSION TAG SEQADV 2DEN HIS A 5 UNP P06654 EXPRESSION TAG SEQADV 2DEN HIS A 6 UNP P06654 EXPRESSION TAG SEQADV 2DEN HIS A 7 UNP P06654 EXPRESSION TAG SEQADV 2DEN GLN A 8 UNP P06654 EXPRESSION TAG SEQADV 2DEN ALA A 12 UNP P06654 ILE 232 ENGINEERED MUTATION SEQADV 2DEN GLY A 63 UNP P06654 LINKER SEQRES 1 A 108 MET HIS HIS HIS HIS HIS HIS GLN TYR LYS LEU ALA LEU SEQRES 2 A 108 ASN GLY LYS THR LEU LYS GLY GLU THR THR THR GLU ALA SEQRES 3 A 108 VAL ASP ALA ALA THR ALA GLU LYS VAL PHE LYS GLN TYR SEQRES 4 A 108 ALA ASN ASP ASN GLY VAL ASP GLY GLU TRP THR TYR ASP SEQRES 5 A 108 ASP ALA THR LYS THR PHE THR VAL THR GLU GLY SER GLN SEQRES 6 A 108 TRP GLN PRO GLN LEU GLN GLN LEU ARG ASP MET GLY ILE SEQRES 7 A 108 GLN ASP ASP GLU LEU SER LEU ARG ALA LEU GLN ALA THR SEQRES 8 A 108 GLY GLY ASP ILE GLN ALA ALA LEU GLU LEU ILE PHE ALA SEQRES 9 A 108 GLY GLY ALA PRO SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HELIX 1 1 TRP A 66 ILE A 78 1 13 HELIX 2 2 ASP A 80 GLY A 92 1 13 HELIX 3 3 ASP A 94 GLY A 105 1 12 HELIX 4 4 THR B 22 GLY B 35 1 14 HELIX 5 5 PRO B 37 ASP B 39 5 3 SHEET 1 A 5 THR B 12 GLU B 16 0 SHEET 2 A 5 GLN B 2 THR B 7 -1 N VAL B 5 O ILE B 13 SHEET 3 A 5 THR B 66 LEU B 71 1 O LEU B 67 N PHE B 4 SHEET 4 A 5 GLN B 41 PHE B 45 -1 N ARG B 42 O VAL B 70 SHEET 5 A 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 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 MODEL 1