HEADER DNA BINDING PROTEIN 28-MAY-04 1WJ2 TITLE SOLUTION STRUCTURE OF THE C-TERMINAL WRKY DOMAIN OF ATWRKY4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE WRKY TRANSCRIPTION FACTOR 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL WRKY DOMAIN; COMPND 5 SYNONYM: WRKY DNA-BINDING PROTEIN 4, WRKY4; COMPND 6 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: WRKY4; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PCR2.1; SOURCE 8 OTHER_DETAILS: CELL-FREE SYNTHESIS KEYWDS DNA-BINDING DOMAIN, ZINC-BINDING, STRUCTURAL GENOMICS, RIKEN KEYWDS 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.YAMASAKI,M.INOUE,T.KIGAWA,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 02-MAR-22 1WJ2 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1WJ2 1 VERSN REVDAT 2 11-OCT-05 1WJ2 1 JRNL REVDAT 1 28-NOV-04 1WJ2 0 JRNL AUTH K.YAMASAKI,T.KIGAWA,M.INOUE,M.TATENO,T.YAMASAKI,T.YABUKI, JRNL AUTH 2 M.AOKI,E.SEKI,T.MATSUDA,Y.TOMO,N.HAYAMI,T.TERADA,M.SHIROUZU, JRNL AUTH 3 A.TANAKA,M.SEKI,K.SHINOZAKI,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF AN ARABIDOPSIS WRKY DNA BINDING JRNL TITL 2 DOMAIN. JRNL REF PLANT CELL V. 17 944 2005 JRNL REFN ISSN 1040-4651 JRNL PMID 15705956 JRNL DOI 10.1105/TPC.104.026435 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 2000, CNS 1.1 REMARK 3 AUTHORS : MSI (FELIX), REMARK 3 BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI, REMARK 3 NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WJ2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000023632. 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 : 0.3M REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM WRKY DOMAIN; 20MM KPI; 300MM REMARK 210 KCL; 0.02MM ZNCL2; 1MM DTT REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 3D_13C REMARK 210 -SEPARATED_NOESY; 3D_15N- REMARK 210 SEPARATED_NOESY; DQF-COSY; HMQC-J REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 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 : 15 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 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 392 REMARK 465 SER A 393 REMARK 465 SER A 394 REMARK 465 GLY A 395 REMARK 465 SER A 396 REMARK 465 SER A 397 REMARK 465 GLY A 398 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 THR A 402 39.41 -140.37 REMARK 500 1 LEU A 408 92.08 -63.08 REMARK 500 1 ASP A 410 31.12 -144.66 REMARK 500 1 CYS A 434 98.86 -64.17 REMARK 500 1 PRO A 437 91.29 -52.76 REMARK 500 1 PRO A 452 65.35 -66.96 REMARK 500 1 LYS A 453 77.74 65.32 REMARK 500 1 ASN A 464 31.64 -144.87 REMARK 500 1 HIS A 465 16.87 -140.51 REMARK 500 1 ASP A 466 176.44 57.34 REMARK 500 1 PRO A 468 172.78 -52.95 REMARK 500 2 ASP A 410 35.05 -164.63 REMARK 500 2 TYR A 417 -46.10 -155.82 REMARK 500 2 PRO A 428 178.50 -50.88 REMARK 500 2 LYS A 453 77.48 -176.65 REMARK 500 2 PRO A 468 -168.51 -55.21 REMARK 500 3 SER A 403 31.41 -98.55 REMARK 500 3 ASP A 406 46.68 -90.95 REMARK 500 3 LEU A 407 44.30 -100.07 REMARK 500 3 LEU A 408 39.39 -97.11 REMARK 500 3 TYR A 417 -46.09 -130.71 REMARK 500 3 LYS A 423 79.10 -66.34 REMARK 500 3 PRO A 437 100.24 -49.52 REMARK 500 3 PRO A 452 66.63 -67.08 REMARK 500 3 LYS A 453 81.48 63.73 REMARK 500 3 ASP A 466 -176.25 50.46 REMARK 500 3 PRO A 468 170.37 -54.28 REMARK 500 4 LEU A 407 97.96 -62.71 REMARK 500 4 ASP A 410 -60.11 -144.27 REMARK 500 4 TYR A 417 -46.20 -130.54 REMARK 500 4 CYS A 434 95.51 -67.05 REMARK 500 4 PRO A 437 88.03 -54.08 REMARK 500 4 LYS A 453 79.55 -177.02 REMARK 500 5 VAL A 405 107.44 -59.96 REMARK 500 5 ASP A 409 103.28 -59.53 REMARK 500 5 ASP A 410 85.85 -167.76 REMARK 500 5 GLN A 419 137.41 -174.27 REMARK 500 5 CYS A 434 98.83 -67.30 REMARK 500 5 PRO A 437 86.79 -55.30 REMARK 500 5 LYS A 453 79.39 -179.76 REMARK 500 5 ASP A 466 177.61 -59.54 REMARK 500 5 PRO A 468 -175.07 -52.88 REMARK 500 6 PRO A 428 -176.61 -51.88 REMARK 500 6 PRO A 437 91.33 -53.10 REMARK 500 6 PRO A 452 65.98 -67.30 REMARK 500 6 LYS A 453 83.55 65.66 REMARK 500 6 PRO A 468 -165.50 -56.35 REMARK 500 7 PRO A 437 91.15 -53.37 REMARK 500 7 PRO A 452 65.13 -67.42 REMARK 500 7 LYS A 453 83.13 64.67 REMARK 500 REMARK 500 THIS ENTRY HAS 126 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 470 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 434 SG REMARK 620 2 CYS A 439 SG 109.5 REMARK 620 3 HIS A 463 ND1 109.0 108.9 REMARK 620 4 HIS A 465 NE2 109.8 110.4 109.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 470 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: ATR001010103.1 RELATED DB: TARGETDB DBREF 1WJ2 A 399 469 UNP Q9XI90 WRKY4_ARATH 399 469 SEQADV 1WJ2 GLY A 392 UNP Q9XI90 CLONING ARTIFACT SEQADV 1WJ2 SER A 393 UNP Q9XI90 CLONING ARTIFACT SEQADV 1WJ2 SER A 394 UNP Q9XI90 CLONING ARTIFACT SEQADV 1WJ2 GLY A 395 UNP Q9XI90 CLONING ARTIFACT SEQADV 1WJ2 SER A 396 UNP Q9XI90 CLONING ARTIFACT SEQADV 1WJ2 SER A 397 UNP Q9XI90 CLONING ARTIFACT SEQADV 1WJ2 GLY A 398 UNP Q9XI90 CLONING ARTIFACT SEQRES 1 A 78 GLY SER SER GLY SER SER GLY VAL GLN THR THR SER GLU SEQRES 2 A 78 VAL ASP LEU LEU ASP ASP GLY TYR ARG TRP ARG LYS TYR SEQRES 3 A 78 GLY GLN LYS VAL VAL LYS GLY ASN PRO TYR PRO ARG SER SEQRES 4 A 78 TYR TYR LYS CYS THR THR PRO GLY CYS GLY VAL ARG LYS SEQRES 5 A 78 HIS VAL GLU ARG ALA ALA THR ASP PRO LYS ALA VAL VAL SEQRES 6 A 78 THR THR TYR GLU GLY LYS HIS ASN HIS ASP LEU PRO ALA HET ZN A 470 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ SHEET 1 A 4 GLY A 418 LYS A 420 0 SHEET 2 A 4 ARG A 429 THR A 435 -1 O ARG A 429 N LYS A 420 SHEET 3 A 4 GLY A 440 ALA A 448 -1 O LYS A 443 N TYR A 432 SHEET 4 A 4 ALA A 454 GLU A 460 -1 O ALA A 454 N ALA A 448 LINK SG CYS A 434 ZN ZN A 470 1555 1555 2.47 LINK SG CYS A 439 ZN ZN A 470 1555 1555 2.47 LINK ND1 HIS A 463 ZN ZN A 470 1555 1555 2.14 LINK NE2 HIS A 465 ZN ZN A 470 1555 1555 2.14 SITE 1 AC1 5 CYS A 434 THR A 436 CYS A 439 HIS A 463 SITE 2 AC1 5 HIS A 465 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