Header list of 2den.pdb file
Complete list - n 15 2 Bytes
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 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
Complete list - n 15 2 Bytes