Header list of 1wr1.pdb file
Complete list - p 9 2 Bytes
HEADER SIGNALING PROTEIN 08-OCT-04 1WR1
TITLE THE COMPLEX STRUCTURE OF DSK2P UBA WITH UBIQUITIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: UBIQUITIN;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: UBIQUITIN-LIKE PROTEIN DSK2;
COMPND 7 CHAIN: B;
COMPND 8 FRAGMENT: C-TERMINAL UBA DOMAIN;
COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE;
SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST;
SOURCE 4 ORGANISM_TAXID: 4932;
SOURCE 5 GENE: UBI4 (1224-1451);
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-24A;
SOURCE 11 MOL_ID: 2;
SOURCE 12 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE;
SOURCE 13 ORGANISM_COMMON: BAKER'S YEAST;
SOURCE 14 ORGANISM_TAXID: 4932;
SOURCE 15 GENE: DSK2 (982-1120);
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: PGEX-KG
KEYWDS UBA DOMAIN, UBA-UBIQUITIN COMPLEX, DSK2, SIGNALING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR A.OHNO,J.G.JEE,K.FUJIWARA,T.TENNO,N.GODA,H.TOCHIO,H.HIROAKI,
AUTHOR 2 H.KOBAYASHI,M.SHIRAKAWA
REVDAT 3 09-SEP-20 1WR1 1 TITLE REMARK SEQADV
REVDAT 2 24-FEB-09 1WR1 1 VERSN
REVDAT 1 19-APR-05 1WR1 0
JRNL AUTH A.OHNO,J.JEE,K.FUJIWARA,T.TENNO,N.GODA,H.TOCHIO,H.KOBAYASHI,
JRNL AUTH 2 H.HIROAKI,M.SHIRAKAWA
JRNL TITL STRUCTURE OF THE UBA DOMAIN OF DSK2P IN COMPLEX WITH
JRNL TITL 2 UBIQUITIN MOLECULAR DETERMINANTS FOR UBIQUITIN RECOGNITION.
JRNL REF STRUCTURE V. 13 521 2005
JRNL REFN ISSN 0969-2126
JRNL PMID 15837191
JRNL DOI 10.1016/J.STR.2005.01.011
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 3.5, AMBER 7
REMARK 3 AUTHORS : PEARLMAN (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1WR1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-OCT-04.
REMARK 100 THE DEPOSITION ID IS D_1000023898.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6.8
REMARK 210 IONIC STRENGTH : 20MM POTASSIUM PHOSPHATE, 5MM
REMARK 210 POTASSIUM CHLORIDE
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : U-15N, 13C UBIQUITIN + DSK2-UBA
REMARK 210 COMPLEX (0.9MM); U-15N, 13C DSK2-
REMARK 210 UBA + UBIQUITIN COMPLEX (1.0MM)
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 4D_13C/15N-SEPARATED_NOESY;
REMARK 210 3D_15N-SEPARATED_NOESY; 3D_13C-SEPARATED_NOESY; 3D_13C-EDITED/
REMARK 210 13C-FILTERED-NOESY; 3D_13C-SEPARATED_ROESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ
REMARK 210 SPECTROMETER MODEL : DRX; INOVA
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : VNMR 6.1C, NMRPIPE 2.1, SPARKY
REMARK 210 3.1.0.0, CYANA 2.0.17
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS,
REMARK 210 SIMULATED ANNEALING, MOLECULAR
REMARK 210 DYNAMICS, ENERGY MINIMIZATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
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 : 16
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: 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 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME;
REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 470 MODELS 1-20
REMARK 470 RES CSSEQI ATOMS
REMARK 470 MET A 1 N
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 1 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 ARG B 331 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 1 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 3 PRO B 316 CA - N - CD ANGL. DEV. = -9.1 DEGREES
REMARK 500 3 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 4 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 4 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 4 PRO B 316 CA - N - CD ANGL. DEV. = -8.8 DEGREES
REMARK 500 4 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 5 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 5 PRO B 316 CA - N - CD ANGL. DEV. = -8.9 DEGREES
REMARK 500 5 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 6 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 6 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 6 ARG B 356 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 7 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 7 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 7 PRO B 316 CA - N - CD ANGL. DEV. = -9.2 DEGREES
REMARK 500 7 ARG B 331 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 7 ARG B 356 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 8 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 9 PRO B 316 CA - N - CD ANGL. DEV. = -9.0 DEGREES
REMARK 500 9 ARG B 356 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 10 ARG B 331 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 11 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 11 PRO B 316 CA - N - CD ANGL. DEV. = -8.9 DEGREES
REMARK 500 12 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 12 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 12 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES
REMARK 500 12 PRO B 316 CA - N - CD ANGL. DEV. = -9.1 DEGREES
REMARK 500 12 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 13 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 13 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES
REMARK 500 13 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 13 ARG B 356 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 14 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 14 PRO B 316 CA - N - CD ANGL. DEV. = -8.9 DEGREES
REMARK 500 14 ARG B 331 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 14 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 16 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 16 ARG B 337 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 16 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 17 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 18 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 18 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES
REMARK 500 18 ARG B 337 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 18 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 19 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 19 PRO B 316 CA - N - CD ANGL. DEV. = -8.9 DEGREES
REMARK 500 19 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 51 ANGLE DEVIATIONS.
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 GLU A 64 19.03 55.93
REMARK 500 1 ARG A 74 -59.60 62.44
REMARK 500 1 SER B 319 -173.65 61.17
REMARK 500 2 ALA A 46 29.94 47.90
REMARK 500 2 ARG A 74 5.32 56.93
REMARK 500 2 ASP B 346 76.31 -66.64
REMARK 500 4 GLU A 64 18.69 56.61
REMARK 500 4 ARG A 74 18.98 53.34
REMARK 500 4 ILE B 325 6.09 -65.85
REMARK 500 5 ALA A 46 27.86 48.41
REMARK 500 5 GLU A 64 22.43 49.41
REMARK 500 6 ALA A 46 47.58 38.66
REMARK 500 6 GLU A 64 19.05 53.35
REMARK 500 6 SER B 319 88.30 -69.53
REMARK 500 7 ILE B 318 -56.82 66.29
REMARK 500 8 GLU A 64 20.58 49.31
REMARK 500 8 ILE B 318 -86.26 44.19
REMARK 500 8 ASP B 346 78.55 -69.81
REMARK 500 9 ALA A 46 28.54 48.79
REMARK 500 9 GLU A 64 20.37 48.51
REMARK 500 10 GLU A 64 21.97 49.46
REMARK 500 10 ILE B 325 71.72 54.52
REMARK 500 11 GLU A 64 22.48 48.77
REMARK 500 11 ARG A 74 -60.95 -132.89
REMARK 500 11 ILE B 325 -2.94 -59.71
REMARK 500 13 GLU A 64 20.74 49.72
REMARK 500 14 GLU A 64 19.00 57.93
REMARK 500 14 ARG A 74 -69.78 54.62
REMARK 500 14 SER B 319 18.87 48.95
REMARK 500 14 ILE B 325 25.15 -75.80
REMARK 500 15 GLU A 64 18.81 54.54
REMARK 500 16 PHE B 344 77.10 -102.29
REMARK 500 18 ARG A 74 -0.29 45.80
REMARK 500 18 ILE B 318 -82.71 52.06
REMARK 500 19 ALA A 46 28.95 47.86
REMARK 500 19 GLU A 64 26.00 47.08
REMARK 500 20 ALA A 46 29.31 48.10
REMARK 500 20 GLU A 64 19.89 50.30
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1D3Z RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF UBIQUITIN
DBREF 1WR1 A 1 76 UNP P61864 UBIQ_YEAST 1 76
DBREF 1WR1 B 328 373 UNP P48510 DSK2_YEAST 328 373
SEQADV 1WR1 PRO B 316 UNP P48510 CLONING ARTIFACT
SEQADV 1WR1 GLY B 317 UNP P48510 CLONING ARTIFACT
SEQADV 1WR1 ILE B 318 UNP P48510 CLONING ARTIFACT
SEQADV 1WR1 SER B 319 UNP P48510 CLONING ARTIFACT
SEQADV 1WR1 GLY B 320 UNP P48510 CLONING ARTIFACT
SEQADV 1WR1 GLY B 321 UNP P48510 CLONING ARTIFACT
SEQADV 1WR1 GLY B 322 UNP P48510 CLONING ARTIFACT
SEQADV 1WR1 GLY B 323 UNP P48510 CLONING ARTIFACT
SEQADV 1WR1 GLY B 324 UNP P48510 CLONING ARTIFACT
SEQADV 1WR1 ILE B 325 UNP P48510 CLONING ARTIFACT
SEQADV 1WR1 LEU B 326 UNP P48510 CLONING ARTIFACT
SEQADV 1WR1 ASP B 327 UNP P48510 CLONING ARTIFACT
SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE
SEQRES 2 A 76 THR LEU GLU VAL GLU SER SER ASP THR ILE ASP ASN VAL
SEQRES 3 A 76 LYS SER 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 58 PRO GLY ILE SER GLY GLY GLY GLY GLY ILE LEU ASP PRO
SEQRES 2 B 58 GLU GLU ARG TYR GLU HIS GLN LEU ARG GLN LEU ASN ASP
SEQRES 3 B 58 MET GLY PHE PHE ASP PHE ASP ARG ASN VAL ALA ALA LEU
SEQRES 4 B 58 ARG ARG SER GLY GLY SER VAL GLN GLY ALA LEU ASP SER
SEQRES 5 B 58 LEU LEU ASN GLY ASP VAL
HELIX 1 1 THR A 22 GLN A 31 1 10
HELIX 2 2 LEU A 56 ASN A 60 5 5
HELIX 3 3 GLY B 323 LEU B 326 5 4
HELIX 4 4 ASP B 327 TYR B 332 1 6
HELIX 5 5 TYR B 332 GLY B 343 1 12
HELIX 6 6 ASP B 346 GLY B 358 1 13
HELIX 7 7 SER B 360 GLY B 371 1 12
SHEET 1 A 5 THR A 12 LEU A 15 0
SHEET 2 A 5 ILE A 3 LYS A 6 -1 N VAL A 5 O ILE A 13
SHEET 3 A 5 SER A 65 LEU A 71 1 O SER A 65 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
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 - p 9 2 Bytes