HEADER DNA BINDING PROTEIN 09-SEP-03 1UL5 TITLE SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN OF SQUAMOSA PROMOTER TITLE 2 BINDING PROTEIN-LIKE 7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA-BINDING DOMAIN (SBP DOMAIN); COMPND 5 SYNONYM: SPL7; 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: SPL7; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PCR2.1; SOURCE 8 OTHER_DETAILS: CELL-FREE SYNTHESIS KEYWDS TRANSCRIPTION FACTOR, SBP, FLOWER DEVELOPMENT, DNA BINDING PROTEIN, KEYWDS 2 STRUCTURAL GENOMICS, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 3 INITIATIVE, RSGI EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.YAMASAKI,M.INOUE,T.KIGAWA,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 27-DEC-23 1UL5 1 REMARK REVDAT 3 02-MAR-22 1UL5 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1UL5 1 VERSN REVDAT 1 09-MAR-04 1UL5 0 JRNL AUTH K.YAMASAKI,T.KIGAWA,M.INOUE,M.TATENO,T.YAMASAKI,T.YABUKI, JRNL AUTH 2 M.AOKI,E.SEKI,T.MATSUDA,E.NUNOKAWA,Y.ISHIZUKA,T.TERADA, JRNL AUTH 3 M.SHIROUZU,T.OSANAI,A.TANAKA,M.SEKI,K.SHINOZAKI,S.YOKOYAMA JRNL TITL A NOVEL ZINC-BINDING MOTIF REVEALED BY SOLUTION STRUCTURES JRNL TITL 2 OF DNA-BINDING DOMAINS OF ARABIDOPSIS SBP-FAMILY JRNL TITL 3 TRANSCRIPTION FACTORS. JRNL REF J.MOL.BIOL. V. 337 49 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15001351 JRNL DOI 10.1016/J.JMB.2004.01.015 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE REMARK 3 -KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON, REMARK 3 WARREN (CNS), BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE, REMARK 3 JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UL5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-SEP-03. REMARK 100 THE DEPOSITION ID IS D_1000005948. 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 : 20MM KPI, 300MM KCL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.02MM ZNCL2 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 3D_13C REMARK 210 -SEPARATED_NOESY; 3D_15N- REMARK 210 SEPARATED_NOESY; HMQC-J; DQF-COSY 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 : NULL 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 LEAST REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 133 REMARK 465 SER A 134 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 ALA A 136 81.18 -63.90 REMARK 500 1 ARG A 137 117.34 -160.06 REMARK 500 1 GLN A 139 42.74 -89.98 REMARK 500 1 ASP A 146 62.57 -115.90 REMARK 500 1 ILE A 147 69.41 -67.89 REMARK 500 1 HIS A 157 23.60 -152.77 REMARK 500 1 SER A 167 -62.62 75.12 REMARK 500 1 LEU A 171 -172.01 -59.56 REMARK 500 1 ASP A 172 92.73 -50.78 REMARK 500 1 LYS A 184 -177.89 -68.46 REMARK 500 1 ASP A 190 42.78 -100.56 REMARK 500 1 LYS A 195 176.51 60.34 REMARK 500 1 ARG A 196 60.70 -107.45 REMARK 500 1 ARG A 204 -48.19 -165.64 REMARK 500 1 ASN A 206 -58.13 -142.68 REMARK 500 1 ASN A 207 31.11 -99.26 REMARK 500 1 VAL A 214 -75.36 -96.80 REMARK 500 1 LYS A 216 -38.50 178.64 REMARK 500 1 VAL A 219 -45.68 -153.44 REMARK 500 2 ALA A 136 99.85 -58.35 REMARK 500 2 CYS A 138 97.98 -62.64 REMARK 500 2 GLN A 139 42.18 -89.10 REMARK 500 2 GLU A 144 77.10 -100.58 REMARK 500 2 ASP A 146 68.59 -117.16 REMARK 500 2 HIS A 157 19.59 -145.45 REMARK 500 2 SER A 167 -64.47 72.98 REMARK 500 2 LEU A 171 -171.21 -59.86 REMARK 500 2 ASP A 172 90.63 -54.61 REMARK 500 2 TYR A 178 95.65 -64.06 REMARK 500 2 ARG A 196 31.62 -98.43 REMARK 500 2 ARG A 199 96.30 -59.61 REMARK 500 2 LYS A 201 100.85 -59.45 REMARK 500 2 ARG A 204 159.87 61.16 REMARK 500 2 ARG A 208 88.92 60.84 REMARK 500 2 ARG A 209 -47.56 -142.90 REMARK 500 2 LYS A 212 84.83 -169.54 REMARK 500 2 ASP A 215 -65.84 -156.16 REMARK 500 2 LYS A 216 99.53 60.75 REMARK 500 3 ARG A 137 114.83 -160.03 REMARK 500 3 CYS A 138 99.98 -57.56 REMARK 500 3 GLN A 139 42.07 -90.09 REMARK 500 3 ASP A 146 66.28 -111.67 REMARK 500 3 GLU A 149 29.97 -153.34 REMARK 500 3 LEU A 171 -172.21 -57.48 REMARK 500 3 ASP A 172 90.75 -54.14 REMARK 500 3 ASP A 190 31.86 -98.51 REMARK 500 3 ASP A 192 -168.48 -78.37 REMARK 500 3 HIS A 205 -61.53 -121.87 REMARK 500 3 ASN A 207 113.60 61.33 REMARK 500 3 ARG A 211 -46.47 -156.62 REMARK 500 REMARK 500 THIS ENTRY HAS 333 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 221 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 138 SG REMARK 620 2 CYS A 143 SG 110.2 REMARK 620 3 CYS A 160 SG 114.7 110.0 REMARK 620 4 CYS A 163 SG 105.5 108.8 107.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 222 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 179 SG REMARK 620 2 CYS A 182 SG 109.6 REMARK 620 3 HIS A 186 NE2 108.1 108.2 REMARK 620 4 CYS A 198 SG 111.3 109.9 109.7 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 221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 222 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: ATR001006152.1 RELATED DB: TARGETDB DBREF 1UL5 A 135 220 UNP Q8S9G8 SPL7_ARATH 135 220 SEQADV 1UL5 GLY A 133 UNP Q8S9G8 CLONING ARTIFACT SEQADV 1UL5 SER A 134 UNP Q8S9G8 CLONING ARTIFACT SEQRES 1 A 88 GLY SER VAL ALA ARG CYS GLN VAL PRO ASP CYS GLU ALA SEQRES 2 A 88 ASP ILE SER GLU LEU LYS GLY TYR HIS LYS ARG HIS ARG SEQRES 3 A 88 VAL CYS LEU ARG CYS ALA THR ALA SER PHE VAL VAL LEU SEQRES 4 A 88 ASP GLY GLU ASN LYS ARG TYR CYS GLN GLN CYS GLY LYS SEQRES 5 A 88 PHE HIS LEU LEU PRO ASP PHE ASP GLU GLY LYS ARG SER SEQRES 6 A 88 CYS ARG ARG LYS LEU GLU ARG HIS ASN ASN ARG ARG LYS SEQRES 7 A 88 ARG LYS PRO VAL ASP LYS GLY GLY VAL ALA HET ZN A 221 1 HET ZN A 222 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 HIS A 154 ARG A 158 5 5 HELIX 2 2 CYS A 160 SER A 167 1 8 HELIX 3 3 PRO A 189 PHE A 191 5 3 SHEET 1 A 2 GLN A 139 VAL A 140 0 SHEET 2 A 2 CYS A 143 GLU A 144 -1 O CYS A 143 N VAL A 140 SHEET 1 B 3 PHE A 168 LEU A 171 0 SHEET 2 B 3 GLU A 174 TYR A 178 -1 N LYS A 176 O VAL A 169 SHEET 3 B 3 PHE A 185 LEU A 187 -1 O HIS A 186 N ARG A 177 LINK SG CYS A 138 ZN ZN A 221 1555 1555 2.46 LINK SG CYS A 143 ZN ZN A 221 1555 1555 2.47 LINK SG CYS A 160 ZN ZN A 221 1555 1555 2.47 LINK SG CYS A 163 ZN ZN A 221 1555 1555 2.46 LINK SG CYS A 179 ZN ZN A 222 1555 1555 2.47 LINK SG CYS A 182 ZN ZN A 222 1555 1555 2.46 LINK NE2 HIS A 186 ZN ZN A 222 1555 1555 2.14 LINK SG CYS A 198 ZN ZN A 222 1555 1555 2.46 SITE 1 AC1 4 CYS A 138 CYS A 143 CYS A 160 CYS A 163 SITE 1 AC2 4 CYS A 179 CYS A 182 HIS A 186 CYS A 198 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