PDB Short entry for 1VDY 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 4 27-DEC-23 1VDY 1 REMARK 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