Header list of 1vdy.pdb file
Complete list - r 2 2 Bytes
HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 25-MAR-04 1VDY
TITLE NMR STRUCTURE OF THE HYPOTHETICAL ENTH-VHS DOMAIN AT3G16270 FROM
TITLE 2 ARABIDOPSIS THALIANA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN (RAFL09-17-B18);
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: ENTH-VHS HYPOTHETICAL DOMAIN;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA;
SOURCE 3 ORGANISM_COMMON: THALE CRESS;
SOURCE 4 ORGANISM_TAXID: 3702;
SOURCE 5 GENE: RIKEN CDNA RAFL09-17-B18;
SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P021216-68;
SOURCE 8 OTHER_DETAILS: E.COLI CELL-FREE PROTEIN SYNTHESIS
KEYWDS HYPOTHETICAL PROTEIN, STRUCTURAL GENOMICS, RIKEN STRUCTURAL
KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, RSGI, UNKNOWN FUNCTION
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR B.LOPEZ-MENDEZ,D.PANTOJA-UCEDA,T.TOMIZAWA,S.KOSHIBA,T.KIGAWA,
AUTHOR 2 M.SHIROUZU,T.TERADA,M.INOUE,T.YABUKI,M.AOKI,E.SEKI,T.MATSUDA,
AUTHOR 3 H.HIROTA,M.YOSHIDA,A.TANAKA,T.OSANAI,M.SEKI,K.SHINOZAKI,S.YOKOYAMA,
AUTHOR 4 P.GUNTERT,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT 3 02-MAR-22 1VDY 1 REMARK SEQADV
REVDAT 2 24-FEB-09 1VDY 1 VERSN
REVDAT 1 03-MAY-05 1VDY 0
JRNL AUTH B.LOPEZ-MENDEZ,D.PANTOJA-UCEDA,T.TOMIZAWA,S.KOSHIBA,
JRNL AUTH 2 T.KIGAWA,M.SHIROUZU,T.TERADA,M.INOUE,T.YABUKI,M.AOKI,E.SEKI,
JRNL AUTH 3 T.MATSUDA,H.HIROTA,M.YOSHIDA,A.TANAKA,T.OSANAI,M.SEKI,
JRNL AUTH 4 K.SHINOZAKI,S.YOKOYAMA,P.GUNTERT
JRNL TITL SOLUTION STRUCTURE OF THE HYPOTHETICAL ENTH-VHS DOMAIN
JRNL TITL 2 AT3G16270 FROM ARABIDOPSIS THALIANA
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH B.LOPEZ-MENDEZ,D.PANTOJA-UCEDA,T.TOMIZAWA,S.KOSHIBA,
REMARK 1 AUTH 2 T.KIGAWA,M.SHIROUZU,T.TERADA,M.INOUE,T.YABUKI,M.AOKI,E.SEKI,
REMARK 1 AUTH 3 T.MATSUDA,H.HIROTA,M.YOSHIDA,A.TANAKA,T.OSANAI,M.SEKI,
REMARK 1 AUTH 4 K.SHINOZAKI,S.YOKOYAMA,P.GUNTERT
REMARK 1 TITL NMR ASSIGNMENT OF THE HYPOTHETICAL ENTH-VHS DOMAIN AT3G16270
REMARK 1 TITL 2 FROM ARABIDOPSIS THALIANA
REMARK 1 REF J.BIOMOL.NMR V. 29 205 2004
REMARK 1 REFN ISSN 0925-2738
REMARK 1 PMID 15014234
REMARK 1 DOI 10.1023/B:JNMR.0000019239.44783.66
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CYANA 2.0.27, OPALP 1.3
REMARK 3 AUTHORS : GUNTERT, P. ET AL. (CYANA), KORADI, R., BILLETER,
REMARK 3 M., GUNTERT, P. (OPALP)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1VDY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAR-04.
REMARK 100 THE DEPOSITION ID IS D_1000006508.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 7.5
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.20MM 13C, 15N-ARABIDOPSIS ENTH
REMARK 210 -VHS HYPOTHETICAL DOMAIN; 20MM
REMARK 210 TRIS BUFFER; 100MM NACL; 1MM
REMARK 210 DITHIOTHREITOL; 0.02% NA3N; 90%
REMARK 210 H2O, 10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C
REMARK 210 -SEPARATED_NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ
REMARK 210 SPECTROMETER MODEL : DRX; AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
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: 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 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 OE1 GLU A 33 HH TYR A 75 1.58
REMARK 500
REMARK 500 REMARK: NULL
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 57 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
REMARK 500 8 ARG A 14 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES
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 LYS A 79 -43.16 -153.24
REMARK 500 1 LEU A 108 -79.43 -71.58
REMARK 500 1 PHE A 129 45.95 -101.59
REMARK 500 2 SER A 6 3.60 -67.25
REMARK 500 2 GLU A 8 27.18 48.17
REMARK 500 2 LYS A 25 108.50 -57.74
REMARK 500 2 SER A 42 -120.24 -94.43
REMARK 500 2 LYS A 79 -33.28 -134.27
REMARK 500 2 LYS A 102 -7.25 -142.09
REMARK 500 2 LEU A 108 -69.11 -94.29
REMARK 500 2 VAL A 117 -72.17 -52.73
REMARK 500 2 SER A 139 -50.03 71.63
REMARK 500 3 SER A 135 -68.77 -144.30
REMARK 500 4 SER A 6 -73.49 -90.77
REMARK 500 4 SER A 92 1.50 -64.60
REMARK 500 4 TYR A 101 109.77 -58.08
REMARK 500 4 LYS A 109 -62.90 -91.93
REMARK 500 4 ASP A 111 5.94 57.45
REMARK 500 4 SER A 135 -80.18 -68.40
REMARK 500 5 SER A 2 7.73 57.64
REMARK 500 5 ASP A 22 13.28 -68.35
REMARK 500 5 LYS A 79 -32.08 -148.81
REMARK 500 5 ARG A 85 -70.53 -64.14
REMARK 500 5 ALA A 112 -61.60 -95.94
REMARK 500 5 PHE A 129 42.47 -107.21
REMARK 500 5 SER A 135 82.71 -169.23
REMARK 500 6 SER A 2 170.44 -56.78
REMARK 500 6 SER A 3 -71.21 -60.84
REMARK 500 6 LYS A 25 101.55 -53.98
REMARK 500 6 LYS A 79 -29.16 -140.18
REMARK 500 6 SER A 92 -6.47 -56.19
REMARK 500 6 ASP A 111 -14.34 63.40
REMARK 500 6 GLU A 132 -179.49 -67.53
REMARK 500 7 TYR A 10 -53.06 -29.24
REMARK 500 7 ASP A 22 38.50 -75.26
REMARK 500 7 LYS A 79 -6.37 -142.59
REMARK 500 7 SER A 82 -28.02 -150.64
REMARK 500 7 HIS A 100 25.26 -141.87
REMARK 500 7 LYS A 102 -39.22 -146.33
REMARK 500 7 LYS A 109 -63.72 -97.97
REMARK 500 7 ASP A 111 34.27 -140.17
REMARK 500 7 PHE A 129 42.14 -107.28
REMARK 500 8 SER A 21 35.06 -66.79
REMARK 500 8 ASP A 22 4.86 58.85
REMARK 500 8 LYS A 102 -4.15 -142.27
REMARK 500 8 LEU A 108 -65.75 -128.30
REMARK 500 8 PRO A 137 77.09 -63.81
REMARK 500 9 GLU A 8 83.84 -68.87
REMARK 500 9 LYS A 79 -18.68 -152.48
REMARK 500 9 LEU A 108 -76.01 -68.57
REMARK 500
REMARK 500 THIS ENTRY HAS 121 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 1 ARG A 90 0.12 SIDE CHAIN
REMARK 500 2 TYR A 10 0.07 SIDE CHAIN
REMARK 500 2 ARG A 86 0.08 SIDE CHAIN
REMARK 500 4 ARG A 57 0.08 SIDE CHAIN
REMARK 500 4 TYR A 75 0.08 SIDE CHAIN
REMARK 500 4 ARG A 86 0.14 SIDE CHAIN
REMARK 500 5 ARG A 118 0.11 SIDE CHAIN
REMARK 500 6 TYR A 10 0.08 SIDE CHAIN
REMARK 500 7 ARG A 57 0.08 SIDE CHAIN
REMARK 500 7 ARG A 118 0.12 SIDE CHAIN
REMARK 500 8 TYR A 10 0.06 SIDE CHAIN
REMARK 500 8 ARG A 12 0.13 SIDE CHAIN
REMARK 500 8 TYR A 75 0.07 SIDE CHAIN
REMARK 500 9 ARG A 118 0.17 SIDE CHAIN
REMARK 500 10 ARG A 57 0.12 SIDE CHAIN
REMARK 500 11 TYR A 10 0.07 SIDE CHAIN
REMARK 500 11 ARG A 57 0.12 SIDE CHAIN
REMARK 500 11 TYR A 75 0.09 SIDE CHAIN
REMARK 500 11 ARG A 90 0.09 SIDE CHAIN
REMARK 500 11 ARG A 118 0.10 SIDE CHAIN
REMARK 500 12 ARG A 12 0.11 SIDE CHAIN
REMARK 500 12 TYR A 75 0.07 SIDE CHAIN
REMARK 500 12 ARG A 118 0.16 SIDE CHAIN
REMARK 500 13 ARG A 12 0.10 SIDE CHAIN
REMARK 500 13 ARG A 40 0.08 SIDE CHAIN
REMARK 500 14 ARG A 57 0.12 SIDE CHAIN
REMARK 500 14 ARG A 85 0.12 SIDE CHAIN
REMARK 500 16 ARG A 14 0.10 SIDE CHAIN
REMARK 500 16 ARG A 40 0.08 SIDE CHAIN
REMARK 500 17 TYR A 10 0.07 SIDE CHAIN
REMARK 500 17 ARG A 12 0.11 SIDE CHAIN
REMARK 500 17 ARG A 118 0.16 SIDE CHAIN
REMARK 500 18 ARG A 12 0.09 SIDE CHAIN
REMARK 500 18 TYR A 75 0.10 SIDE CHAIN
REMARK 500 19 ARG A 14 0.13 SIDE CHAIN
REMARK 500 19 ARG A 90 0.09 SIDE CHAIN
REMARK 500 20 ARG A 86 0.08 SIDE CHAIN
REMARK 500 20 ARG A 118 0.08 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5928 RELATED DB: BMRB
REMARK 900 CHEMICAL SHIFT DATA
REMARK 900 RELATED ID: ATR001000337 RELATED DB: TARGETDB
DBREF 1VDY A 8 134 UNP Q9C5H4 Q9C5H4_ARATH 9 135
SEQADV 1VDY GLY A 1 UNP Q9C5H4 CLONING ARTIFACT
SEQADV 1VDY SER A 2 UNP Q9C5H4 CLONING ARTIFACT
SEQADV 1VDY SER A 3 UNP Q9C5H4 CLONING ARTIFACT
SEQADV 1VDY GLY A 4 UNP Q9C5H4 CLONING ARTIFACT
SEQADV 1VDY SER A 5 UNP Q9C5H4 CLONING ARTIFACT
SEQADV 1VDY SER A 6 UNP Q9C5H4 CLONING ARTIFACT
SEQADV 1VDY GLY A 7 UNP Q9C5H4 CLONING ARTIFACT
SEQADV 1VDY SER A 135 UNP Q9C5H4 CLONING ARTIFACT
SEQADV 1VDY GLY A 136 UNP Q9C5H4 CLONING ARTIFACT
SEQADV 1VDY PRO A 137 UNP Q9C5H4 CLONING ARTIFACT
SEQADV 1VDY SER A 138 UNP Q9C5H4 CLONING ARTIFACT
SEQADV 1VDY SER A 139 UNP Q9C5H4 CLONING ARTIFACT
SEQADV 1VDY GLY A 140 UNP Q9C5H4 CLONING ARTIFACT
SEQRES 1 A 140 GLY SER SER GLY SER SER GLY GLU SER TYR TRP ARG SER
SEQRES 2 A 140 ARG MET ILE ASP ALA VAL THR SER ASP GLU ASP LYS VAL
SEQRES 3 A 140 ALA PRO VAL TYR LYS LEU GLU GLU ILE CYS ASP LEU LEU
SEQRES 4 A 140 ARG SER SER HIS VAL SER ILE VAL LYS GLU PHE SER GLU
SEQRES 5 A 140 PHE ILE LEU LYS ARG LEU ASP ASN LYS SER PRO ILE VAL
SEQRES 6 A 140 LYS GLN LYS ALA LEU ARG LEU ILE LYS TYR ALA VAL GLY
SEQRES 7 A 140 LYS SER GLY SER GLU PHE ARG ARG GLU MET GLN ARG ASN
SEQRES 8 A 140 SER VAL ALA VAL ARG ASN LEU PHE HIS TYR LYS GLY HIS
SEQRES 9 A 140 PRO ASP PRO LEU LYS GLY ASP ALA LEU ASN LYS ALA VAL
SEQRES 10 A 140 ARG GLU THR ALA HIS GLU THR ILE SER ALA ILE PHE SER
SEQRES 11 A 140 GLU GLU ASN GLY SER GLY PRO SER SER GLY
HELIX 1 1 GLU A 8 VAL A 19 1 12
HELIX 2 2 PRO A 28 SER A 42 1 15
HELIX 3 3 HIS A 43 ASP A 59 1 17
HELIX 4 4 SER A 62 VAL A 77 1 16
HELIX 5 5 GLY A 81 ASN A 91 1 11
HELIX 6 6 SER A 92 ASN A 97 1 6
HELIX 7 7 ALA A 112 PHE A 129 1 18
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 - r 2 2 Bytes