10 20 30 40 50 60 70 80 1WJ2 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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, KEYWDS 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, DNA KEYWDS 3 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 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, JRNL AUTH 2 T.YABUKI,M.AOKI,E.SEKI,T.MATSUDA,Y.TOMO,N.HAYAMI, JRNL AUTH 3 T.TERADA,M.SHIROUZU,A.TANAKA,M.SEKI,K.SHINOZAKI, JRNL AUTH 4 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF AN ARABIDOPSIS WRKY DNA JRNL TITL 2 BINDING 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 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, REMARK 3 RICE,SIMONSON,WARREN 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 RCSB ID CODE IS RCSB023632.
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 : 1ATM REMARK 210 SAMPLE CONTENTS : 1MM WRKY DOMAIN; 20MM KPI; REMARK 210 300MM KCL; 0.02MM ZNCL2; 1MM REMARK 210 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, REMARK 210 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 : FELIX 2000, 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 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 7 PRO A 468 -168.82 -55.24 REMARK 500 8 PRO A 437 92.54 -54.30 REMARK 500 8 LYS A 453 81.78 -176.73 REMARK 500 8 ASN A 464 38.73 -141.95 REMARK 500 9 ASP A 406 -71.88 -91.09 REMARK 500 9 PRO A 437 93.52 -48.78 REMARK 500 9 LYS A 453 75.81 179.96 REMARK 500 10 THR A 402 -64.79 -167.34 REMARK 500 10 TYR A 417 -46.32 -137.51 REMARK 500 10 PRO A 428 -169.70 -54.92 REMARK 500 10 CYS A 434 95.02 -66.97 REMARK 500 10 PRO A 437 90.92 -51.31 REMARK 500 10 LYS A 453 76.93 -177.07 REMARK 500 10 PRO A 468 176.74 -54.64 REMARK 500 11 TYR A 417 -47.30 -141.72 REMARK 500 11 PRO A 428 175.24 -50.22 REMARK 500 11 PRO A 437 89.47 -52.58 REMARK 500 11 LYS A 453 77.91 -179.91 REMARK 500 12 ASP A 406 54.87 -92.10 REMARK 500 12 LEU A 407 39.92 -99.09 REMARK 500 12 PRO A 428 -167.94 -56.06 REMARK 500 12 LYS A 433 122.92 -170.03 REMARK 500 12 PRO A 452 68.07 -66.91 REMARK 500 12 LYS A 453 83.41 63.19 REMARK 500 12 ASN A 464 35.13 -98.26 REMARK 500 12 PRO A 468 178.20 -52.73 REMARK 500 13 GLU A 404 51.58 -90.72 REMARK 500 13 TYR A 417 -46.50 -138.52 REMARK 500 13 PRO A 428 -174.70 -52.73 REMARK 500 13 CYS A 434 93.29 -65.79 REMARK 500 13 PRO A 437 90.59 -51.89 REMARK 500 13 LYS A 453 77.23 -177.17 REMARK 500 13 PRO A 468 -178.95 -69.03 REMARK 500 14 ASP A 410 -169.83 -112.78 REMARK 500 14 TYR A 417 -46.77 -133.29 REMARK 500 14 PRO A 428 -162.74 -57.32 REMARK 500 14 CYS A 434 98.32 -68.60 REMARK 500 14 LYS A 453 80.01 -178.17 REMARK 500 15 VAL A 405 97.97 -66.58 REMARK 500 15 ASP A 409 91.66 -63.94 REMARK 500 15 ASP A 410 -74.05 -123.42 REMARK 500 15 PRO A 437 89.40 -52.83 REMARK 500 15 LYS A 453 76.25 -178.95 REMARK 500 16 CYS A 434 96.31 -64.68 REMARK 500 16 PRO A 437 88.82 -53.93 REMARK 500 16 PRO A 452 65.38 -67.06 REMARK 500 16 LYS A 453 78.60 64.78 REMARK 500 16 HIS A 465 18.06 -143.24 REMARK 500 16 ASP A 466 -178.18 54.81 REMARK 500 17 LEU A 407 77.59 -68.40 REMARK 500 17 ASP A 410 35.22 -164.79 REMARK 500 17 PRO A 428 173.14 -50.28 REMARK 500 17 LYS A 433 135.06 -170.05 REMARK 500 17 PRO A 437 90.12 -52.19 REMARK 500 17 PRO A 452 66.20 -67.28 REMARK 500 17 LYS A 453 85.77 67.42 REMARK 500 17 PRO A 468 -178.22 -53.44 REMARK 500 18 THR A 402 -73.25 -155.84 REMARK 500 18 GLU A 404 39.96 -97.11 REMARK 500 18 ASP A 410 87.21 -166.14 REMARK 500 18 TYR A 417 -46.15 -130.18 REMARK 500 18 PRO A 428 169.66 -49.98 REMARK 500 18 PRO A 437 98.32 -50.22 REMARK 500 18 PRO A 452 66.56 -67.05 REMARK 500 18 LYS A 453 81.90 61.59 REMARK 500 18 LEU A 467 109.74 -58.99 REMARK 500 18 PRO A 468 -170.40 -55.44 REMARK 500 19 THR A 401 -70.33 -128.67 REMARK 500 19 THR A 402 95.64 -169.95 REMARK 500 19 TYR A 417 -47.04 -138.72 REMARK 500 19 CYS A 434 98.47 -66.35 REMARK 500 19 PRO A 437 89.56 -52.60 REMARK 500 19 LYS A 453 76.16 -178.56 REMARK 500 19 PRO A 468 -177.55 -54.80 REMARK 500 20 PRO A 437 89.66 -53.16 REMARK 500 20 LYS A 453 77.56 -178.56 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 1 ZN A 470 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 463 ND1 REMARK 620 2 HIS A 465 NE2 109.1 REMARK 620 3 CYS A 434 SG 109.0 109.8 REMARK 620 4 CYS A 439 SG 108.9 110.4 109.5 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 ZN ZN A 470 ND1 HIS A 463 1555 1555 2.14 LINK ZN ZN A 470 NE2 HIS A 465 1555 1555 2.14 LINK ZN ZN A 470 SG CYS A 434 1555 1555 2.47 LINK ZN ZN A 470 SG CYS A 439 1555 1555 2.47
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