HEADER TRANSCRIPTION 12-SEP-20 7D11 TITLE SOLUTION STRUCTURE OF A WKRY DNA-BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: WRKY TRANSCRIPTION FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRANSCRIPTION FACTOR ZAP1,WRKY DNA-BINDING PROTEIN 1,ZINC- COMPND 5 DEPENDENT ACTIVATOR PROTEIN 1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: WRKY1, ZAP1, AT2G04880, F1O13.1, F28I8.34; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCROPTION FACTOR, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Q.W.LI,Y.F.HU,C.W.JIN REVDAT 3 15-MAY-24 7D11 1 REMARK REVDAT 2 14-JUN-23 7D11 1 REMARK REVDAT 1 15-SEP-21 7D11 0 JRNL AUTH Q.W.LI,Y.F.HU,C.W.JIN JRNL TITL STRUCTURE OF A WKRY DNA-BINDING DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7D11 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300017783. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 125 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.8 MM [U-95% 15N] WRKY1-N, 5 % REMARK 210 V/V [U-99% 2H] D2O, 95 % V/V H2O, REMARK 210 25 MM HEPES, 100 MM SODIUM REMARK 210 CHLORIDE, 20 UM ZNCL2, 10 MM DTT, REMARK 210 2 % V/V PROTEASE INHIBITOR, 0.2 REMARK 210 % V/V SODIUM AZIDE, 95% H2O/5% REMARK 210 D2O; 1.8 MM [U-95% 13C; U-95% REMARK 210 15N] WRKY1-N, 5 % V/V [U-99% 2H] REMARK 210 D2O, 95 % V/V H2O, 25 MM HEPES, REMARK 210 100 MM SODIUM CHLORIDE, 20 UM REMARK 210 ZNCL2, 10 MM DTT, 5 % V/V DSS, 2 REMARK 210 % V/V PROTEASE INHIBITOR, 0.2 % REMARK 210 V/V SODIUM AZIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-13C HSQC AROMATIC; 3D HNCA; REMARK 210 3D HN(CO)CA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HBHA(CO)NH; 3D REMARK 210 HNCO; 3D C(CO)NH; 3D H(CCO)NH; REMARK 210 3D HCCH-COSY; 3D CCH-TOCSY; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA, SANE, CANDID, NMRVIEW, REMARK 210 NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 : 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 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 LEU A 80 REMARK 465 VAL A 81 REMARK 465 PRO A 82 REMARK 465 ARG A 83 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 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 ARG A 15 28.43 41.37 REMARK 500 1 GLU A 16 19.82 45.94 REMARK 500 1 GLU A 20 104.15 165.56 REMARK 500 1 ALA A 60 119.31 -14.47 REMARK 500 1 GLN A 63 151.54 63.53 REMARK 500 2 GLU A 20 59.18 110.99 REMARK 500 2 LYS A 34 95.00 55.59 REMARK 500 2 HIS A 47 105.47 -55.94 REMARK 500 2 ALA A 52 112.46 1.43 REMARK 500 3 VAL A 18 -1.28 -59.73 REMARK 500 3 GLN A 30 118.06 170.71 REMARK 500 3 ALA A 60 139.32 -35.40 REMARK 500 3 LYS A 77 -67.30 -101.24 REMARK 500 4 LYS A 17 108.35 -57.82 REMARK 500 4 HIS A 75 79.72 9.33 REMARK 500 4 LYS A 77 75.74 93.53 REMARK 500 5 LYS A 34 61.89 62.37 REMARK 500 5 LYS A 77 86.35 179.68 REMARK 500 6 VAL A 18 135.89 -18.09 REMARK 500 6 HIS A 47 107.66 -51.09 REMARK 500 6 GLU A 72 150.50 -49.20 REMARK 500 7 SER A 11 121.29 -17.19 REMARK 500 7 VAL A 18 91.06 26.21 REMARK 500 7 LYS A 34 83.44 53.65 REMARK 500 7 ASP A 66 144.52 -170.33 REMARK 500 7 HIS A 75 70.53 -119.18 REMARK 500 8 SER A 11 -61.65 -122.66 REMARK 500 8 VAL A 18 140.12 -20.81 REMARK 500 8 LYS A 34 37.51 90.74 REMARK 500 8 ASN A 36 9.11 80.32 REMARK 500 8 HIS A 47 120.83 92.91 REMARK 500 8 HIS A 75 158.12 48.01 REMARK 500 9 LYS A 17 82.68 -52.71 REMARK 500 9 LYS A 27 105.56 -56.13 REMARK 500 9 GLN A 63 128.88 87.32 REMARK 500 10 SER A 11 -71.72 177.74 REMARK 500 10 VAL A 18 78.88 44.44 REMARK 500 10 HIS A 47 109.26 -55.15 REMARK 500 10 ALA A 52 108.25 3.29 REMARK 500 10 ALA A 60 136.89 -34.01 REMARK 500 10 HIS A 75 74.78 29.70 REMARK 500 11 VAL A 18 -167.46 47.63 REMARK 500 11 GLU A 20 71.16 173.58 REMARK 500 11 LYS A 34 90.08 49.77 REMARK 500 11 HIS A 47 122.71 96.80 REMARK 500 11 HIS A 75 70.20 5.19 REMARK 500 11 LYS A 77 74.48 -173.88 REMARK 500 12 VAL A 18 134.79 -15.90 REMARK 500 13 SER A 11 125.68 57.90 REMARK 500 13 VAL A 18 123.42 -15.97 REMARK 500 REMARK 500 THIS ENTRY HAS 82 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 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 45 SG REMARK 620 2 CYS A 50 SG 109.3 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36381 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF A WKRY DNA-BINDING DOMAIN DBREF 7D11 A 2 79 UNP Q9SI37 WRKY1_ARATH 93 170 SEQADV 7D11 MET A 1 UNP Q9SI37 INITIATING METHIONINE SEQADV 7D11 LEU A 80 UNP Q9SI37 EXPRESSION TAG SEQADV 7D11 VAL A 81 UNP Q9SI37 EXPRESSION TAG SEQADV 7D11 PRO A 82 UNP Q9SI37 EXPRESSION TAG SEQADV 7D11 ARG A 83 UNP Q9SI37 EXPRESSION TAG SEQRES 1 A 83 MET SER LEU GLN SER GLY SER GLU GLY ASN SER PRO PHE SEQRES 2 A 83 ILE ARG GLU LYS VAL MET GLU ASP GLY TYR ASN TRP ARG SEQRES 3 A 83 LYS TYR GLY GLN LYS LEU VAL LYS GLY ASN GLU PHE VAL SEQRES 4 A 83 ARG SER TYR TYR ARG CYS THR HIS PRO ASN CYS LYS ALA SEQRES 5 A 83 LYS LYS GLN LEU GLU ARG SER ALA GLY GLY GLN VAL VAL SEQRES 6 A 83 ASP THR VAL TYR PHE GLY GLU HIS ASP HIS PRO LYS PRO SEQRES 7 A 83 LEU LEU VAL PRO ARG HET ZN A 101 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ SHEET 1 AA1 4 TRP A 25 VAL A 33 0 SHEET 2 AA1 4 PHE A 38 CYS A 45 -1 O ARG A 40 N LYS A 31 SHEET 3 AA1 4 LYS A 53 SER A 59 -1 O LYS A 54 N TYR A 43 SHEET 4 AA1 4 VAL A 64 PHE A 70 -1 O PHE A 70 N LYS A 53 LINK SG CYS A 45 ZN ZN A 101 1555 1555 2.80 LINK SG CYS A 50 ZN ZN A 101 1555 1555 2.80 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