10 20 30 40 50 60 70 80 1WH2 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 28-MAY-04 1WH2
TITLE SOLUTION STRUCTURE OF THE GYF DOMAIN OF A HYPOTHETICAL TITLE 2 PROTEIN FROM ARABIDOPSIS THALIANA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN AT5G08430; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GYF 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 RAFL09-47-K03; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P030107-37; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS
KEYWDS GYF DOMAIN, STRUCTURAL GENOMICS, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, RSGI, UNKNOWN FUNCTION
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR N.NAMEKI,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT 2 24-FEB-09 1WH2 1 VERSN REVDAT 1 28-NOV-04 1WH2 0
JRNL AUTH N.NAMEKI,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE GYF DOMAIN OF A JRNL TITL 2 HYPOTHETICAL PROTEIN FROM ARABIDOPSIS THALIANA JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPALP REMARK 3 AUTHORS : KORADI, R.,BILLETER, M.,GUENTERT, P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1WH2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUN-04. REMARK 100 THE RCSB ID CODE IS RCSB023572.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.4MM GYF DOMAIN U-15N, 13C; REMARK 210 20MM PHOSPHATE BUFFER NA; REMARK 210 100MM NACL; 1MM D-DTT; 0.02% REMARK 210 NAN3; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 3D_ REMARK 210 13C-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, NMRPIPE REMARK 210 20020425, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.901, CYANA 1.0.7 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 RESTRAINED MOLECULAR 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 STRUCTURES WITH THE LOWEST REMARK 210 ENERGY, TARGET FUNCTION 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 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 52 NE - CZ - NH1 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 SER A 5 111.26 105.17 REMARK 500 1 VAL A 8 94.23 -61.20 REMARK 500 1 THR A 56 97.44 -61.01 REMARK 500 1 SER A 77 84.97 56.11 REMARK 500 2 VAL A 8 90.93 -66.46 REMARK 500 2 PHE A 47 -157.20 -126.55 REMARK 500 2 SER A 77 146.32 72.23 REMARK 500 3 SER A 2 52.99 37.10 REMARK 500 3 LEU A 11 86.14 -155.84 REMARK 500 3 LEU A 18 96.30 -66.02 REMARK 500 3 SER A 73 47.37 -93.33 REMARK 500 4 SER A 6 177.16 -58.74 REMARK 500 4 VAL A 8 153.64 69.56 REMARK 500 4 LEU A 11 69.77 -107.85 REMARK 500 5 SER A 5 -50.77 -140.98 REMARK 500 5 PRO A 25 39.02 -78.92 REMARK 500 5 SER A 73 98.82 -67.22 REMARK 500 6 SER A 5 76.21 -109.04 REMARK 500 6 VAL A 8 82.77 -61.40 REMARK 500 6 TYR A 46 11.45 -67.98 REMARK 500 7 SER A 2 90.69 -62.59 REMARK 500 7 VAL A 8 107.82 -51.12 REMARK 500 7 SER A 77 77.89 30.33 REMARK 500 8 SER A 3 -171.60 58.47 REMARK 500 8 SER A 5 177.02 58.37 REMARK 500 8 SER A 6 18.61 53.99 REMARK 500 8 VAL A 8 133.17 69.09 REMARK 500 8 PRO A 25 45.02 -80.24 REMARK 500 8 LEU A 72 0.16 -69.66 REMARK 500 8 SER A 77 -161.64 52.27 REMARK 500 9 SER A 5 71.31 33.21 REMARK 500 9 SER A 6 107.94 -54.40 REMARK 500 9 VAL A 8 -155.90 -124.78 REMARK 500 9 GLU A 16 -72.46 -100.10 REMARK 500 9 PHE A 47 -161.92 -122.74 REMARK 500 9 GLN A 50 48.74 -144.08 REMARK 500 10 SER A 2 -173.80 -67.82 REMARK 500 10 SER A 3 -158.14 -147.59 REMARK 500 10 SER A 5 95.87 48.06 REMARK 500 10 SER A 73 48.17 -80.65 REMARK 500 11 SER A 3 -162.78 -109.59 REMARK 500 11 SER A 5 -161.34 -66.74 REMARK 500 11 VAL A 8 56.66 -97.74 REMARK 500 11 PRO A 25 40.38 -86.24 REMARK 500 11 GLN A 50 28.44 -142.06 REMARK 500 11 THR A 56 102.46 -54.13 REMARK 500 11 SER A 77 -19.93 -165.07 REMARK 500 12 VAL A 10 156.96 58.91 REMARK 500 12 ALA A 44 13.45 -69.89 REMARK 500 12 TYR A 46 9.14 -64.88 REMARK 500 12 SER A 73 44.14 -93.44 REMARK 500 13 ARG A 9 -159.54 44.33 REMARK 500 13 LEU A 11 88.01 -150.05 REMARK 500 13 GLN A 50 48.60 -142.19 REMARK 500 13 SER A 73 62.98 -110.72 REMARK 500 14 SER A 2 -89.25 60.57 REMARK 500 14 VAL A 8 -144.85 -125.88 REMARK 500 14 ASP A 14 99.03 -62.46 REMARK 500 14 PHE A 47 -158.79 -116.87 REMARK 500 14 LYS A 49 2.32 -68.62 REMARK 500 15 SER A 3 -169.98 57.57 REMARK 500 15 GLN A 50 40.10 -143.52 REMARK 500 16 SER A 5 78.62 60.03 REMARK 500 16 ASN A 19 10.55 -150.56 REMARK 500 16 SER A 73 44.80 -96.55 REMARK 500 16 PRO A 75 -167.56 -73.32 REMARK 500 16 SER A 77 158.11 70.43 REMARK 500 17 TYR A 46 9.09 -66.05 REMARK 500 18 ARG A 9 172.02 56.48 REMARK 500 18 PHE A 47 -148.09 -115.53 REMARK 500 18 GLN A 50 35.47 -80.15 REMARK 500 19 SER A 5 -95.73 39.26 REMARK 500 19 ARG A 9 8.64 44.73 REMARK 500 19 GLN A 30 -158.95 -80.95 REMARK 500 19 SER A 76 105.33 66.00 REMARK 500 20 ARG A 9 46.94 33.48 REMARK 500 20 SER A 76 104.82 -57.88 REMARK 500 20 SER A 77 78.75 11.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 77 GLY A 78 2 147.21 REMARK 500 SER A 77 GLY A 78 12 -140.41 REMARK 500 GLN A 30 GLY A 31 19 146.49 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 52 0.08 SIDE_CHAIN REMARK 500 3 ARG A 52 0.08 SIDE_CHAIN REMARK 500 4 TYR A 22 0.07 SIDE_CHAIN REMARK 500 5 ARG A 9 0.09 SIDE_CHAIN REMARK 500 8 ARG A 71 0.10 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: ATR001006188.2 RELATED DB: TARGETDB
DBREF 1WH2 A 8 72 UNP Q9FT92 Y5843_ARATH 444 508
SEQADV 1WH2 GLY A 1 UNP Q9FT92 CLONING ARTIFACT SEQADV 1WH2 SER A 2 UNP Q9FT92 CLONING ARTIFACT SEQADV 1WH2 SER A 3 UNP Q9FT92 CLONING ARTIFACT SEQADV 1WH2 GLY A 4 UNP Q9FT92 CLONING ARTIFACT SEQADV 1WH2 SER A 5 UNP Q9FT92 CLONING ARTIFACT SEQADV 1WH2 SER A 6 UNP Q9FT92 CLONING ARTIFACT SEQADV 1WH2 GLY A 7 UNP Q9FT92 CLONING ARTIFACT SEQADV 1WH2 SER A 73 UNP Q9FT92 CLONING ARTIFACT SEQADV 1WH2 GLY A 74 UNP Q9FT92 CLONING ARTIFACT SEQADV 1WH2 PRO A 75 UNP Q9FT92 CLONING ARTIFACT SEQADV 1WH2 SER A 76 UNP Q9FT92 CLONING ARTIFACT SEQADV 1WH2 SER A 77 UNP Q9FT92 CLONING ARTIFACT SEQADV 1WH2 GLY A 78 UNP Q9FT92 CLONING ARTIFACT
SEQRES 1 A 78 GLY SER SER GLY SER SER GLY VAL ARG VAL LEU SER TYR SEQRES 2 A 78 ASP LYS GLU LYS LEU ASN TRP LEU TYR LYS ASP PRO GLN SEQRES 3 A 78 GLY LEU VAL GLN GLY PRO PHE SER LEU THR GLN LEU LYS SEQRES 4 A 78 ALA TRP SER ASP ALA GLU TYR PHE THR LYS GLN PHE ARG SEQRES 5 A 78 VAL TRP MET THR GLY GLU SER MET GLU SER ALA VAL LEU SEQRES 6 A 78 LEU THR ASP VAL LEU ARG LEU SER GLY PRO SER SER GLY
HELIX 1 1 SER A 34 ASP A 43 1 10 HELIX 2 2 LEU A 66 SER A 73 1 8
SHEET 1 A 4 VAL A 29 PHE A 33 0 SHEET 2 A 4 TRP A 20 LYS A 23 -1 N TYR A 22 O GLN A 30 SHEET 3 A 4 ARG A 52 MET A 55 -1 O TRP A 54 N LEU A 21 SHEET 4 A 4 VAL A 64 LEU A 65 -1 O VAL A 64 N VAL A 53
CISPEP 1 GLY A 31 PRO A 32 1 9.01 CISPEP 2 GLY A 31 PRO A 32 2 1.02 CISPEP 3 GLY A 31 PRO A 32 3 9.07 CISPEP 4 GLY A 31 PRO A 32 4 18.58 CISPEP 5 GLY A 31 PRO A 32 5 8.63 CISPEP 6 GLY A 31 PRO A 32 6 -2.58 CISPEP 7 GLY A 31 PRO A 32 7 8.01 CISPEP 8 GLY A 31 PRO A 32 8 21.27 CISPEP 9 GLY A 31 PRO A 32 9 12.24 CISPEP 10 GLY A 31 PRO A 32 10 15.18 CISPEP 11 GLY A 31 PRO A 32 11 10.57 CISPEP 12 GLY A 31 PRO A 32 12 10.57 CISPEP 13 GLY A 31 PRO A 32 13 19.39 CISPEP 14 GLY A 31 PRO A 32 14 9.71 CISPEP 15 GLY A 31 PRO A 32 15 4.71 CISPEP 16 GLY A 31 PRO A 32 16 6.49 CISPEP 17 GLY A 31 PRO A 32 17 -3.86 CISPEP 18 GLY A 31 PRO A 32 18 11.61 CISPEP 19 GLY A 31 PRO A 32 19 7.53 CISPEP 20 GLY A 31 PRO A 32 20 20.20
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