10 20 30 40 50 60 70 80 1WJ0 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA BINDING PROTEIN 28-MAY-04 1WJ0
TITLE SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN OF SQUAMOSA TITLE 2 PROMOTER BINDING PROTEIN-LIKE 12 LACKING THE SECOND ZINC- TITLE 3 BINDING SITE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 12; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA-BINDING DOMAIN (SHORT FRAGMENT); COMPND 5 SYNONYM: SPL12, TRANSCRIPTION FACTOR SPL12; 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: SPL12; 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, STRUCTURAL GENOMICS, RIKEN STRUCTURAL KEYWDS 2 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 3 24-FEB-09 1WJ0 1 VERSN REVDAT 2 21-DEC-04 1WJ0 1 JRNL REVDAT 1 28-NOV-04 1WJ0 0
JRNL AUTH K.YAMASAKI,T.KIGAWA,M.INOUE,T.YAMASAKI,T.YABUKI, JRNL AUTH 2 M.AOKI,E.SEKI,T.MATSUDA,Y.TOMO,T.TERADA,M.SHIROUZU, JRNL AUTH 3 A.TANAKA,M.SEKI,K.SHINOZAKI,S.YOKOYAMA JRNL TITL STRUCTURE OF THE SBP DOMAIN THAT LACKS THE SECOND JRNL TITL 2 ZINC-BINDING SITE JRNL REF TO BE PUBLISHED JRNL REFN
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 1WJ0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-JUN-04. REMARK 100 THE RCSB ID CODE IS RCSB023630.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.3M REMARK 210 PRESSURE : 1ATM REMARK 210 SAMPLE CONTENTS : 1MM SPL12-DBD FRAGMENT; 20MM REMARK 210 KPI; 300MM KCL; 0.02MM ZNCL2; REMARK 210 1MM DTT; 95% H2O; 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 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 : 9 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 122 REMARK 465 SER A 123
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 ASP A 141 -174.84 -175.90 REMARK 500 1 TYR A 142 -67.51 68.55 REMARK 500 1 LYS A 147 86.99 50.20 REMARK 500 1 VAL A 148 136.65 -178.63 REMARK 500 1 ILE A 151 -70.01 -62.29 REMARK 500 1 SER A 172 69.58 62.08 REMARK 500 1 ARG A 173 149.20 -175.06 REMARK 500 1 LEU A 177 38.61 -95.98 REMARK 500 2 CYS A 132 -66.89 -159.78 REMARK 500 2 LYS A 138 38.31 -96.39 REMARK 500 2 LYS A 140 -79.73 -98.12 REMARK 500 2 TYR A 142 -65.44 69.41 REMARK 500 2 ARG A 144 -61.79 -152.19 REMARK 500 2 LYS A 147 81.39 64.85 REMARK 500 2 VAL A 148 133.24 -178.91 REMARK 500 2 ILE A 151 -68.45 -104.41 REMARK 500 2 VAL A 176 179.38 -51.79 REMARK 500 2 LEU A 177 30.60 -96.77 REMARK 500 3 LYS A 140 -78.18 -75.44 REMARK 500 3 ASP A 141 -42.10 -167.63 REMARK 500 3 HIS A 143 34.45 -99.75 REMARK 500 3 ARG A 144 -63.18 -124.58 REMARK 500 3 LYS A 147 64.41 61.49 REMARK 500 3 CYS A 149 -167.53 -67.56 REMARK 500 4 LEU A 136 50.47 -91.49 REMARK 500 4 VAL A 139 173.13 -57.31 REMARK 500 4 LYS A 140 -74.07 -71.27 REMARK 500 4 ASP A 141 -41.91 -169.71 REMARK 500 4 HIS A 143 37.62 -98.82 REMARK 500 4 ARG A 144 -64.86 -130.40 REMARK 500 4 LYS A 154 30.16 -148.49 REMARK 500 4 VAL A 176 174.38 -49.17 REMARK 500 4 LEU A 177 40.56 -95.35 REMARK 500 5 LEU A 136 45.11 -107.72 REMARK 500 5 LYS A 138 41.36 -107.22 REMARK 500 5 LYS A 140 -82.71 -68.16 REMARK 500 5 ASP A 141 -43.85 178.39 REMARK 500 5 SER A 172 70.03 59.92 REMARK 500 5 ARG A 173 133.60 -176.54 REMARK 500 5 VAL A 176 178.76 -53.86 REMARK 500 5 GLU A 178 31.57 -99.83 REMARK 500 5 GLU A 179 -43.09 -164.86 REMARK 500 5 PHE A 180 105.20 -59.21 REMARK 500 6 GLN A 128 40.94 -94.64 REMARK 500 6 LYS A 138 32.00 -96.69 REMARK 500 6 ASP A 141 -177.77 -174.44 REMARK 500 6 HIS A 143 -45.41 -161.80 REMARK 500 6 LYS A 147 75.66 66.24 REMARK 500 6 VAL A 148 134.76 -179.40 REMARK 500 6 HIS A 152 33.72 -96.40 REMARK 500 6 VAL A 176 171.38 -48.42 REMARK 500 7 LEU A 136 41.03 -95.49 REMARK 500 7 LYS A 138 30.98 -97.58 REMARK 500 7 LYS A 140 -78.23 -106.08 REMARK 500 7 HIS A 143 -45.10 -162.97 REMARK 500 7 LYS A 147 75.57 62.62 REMARK 500 7 VAL A 148 139.35 179.73 REMARK 500 7 ALA A 158 130.86 -175.33 REMARK 500 7 LEU A 177 51.06 -91.44 REMARK 500 8 LEU A 136 45.07 -94.55 REMARK 500 8 LYS A 138 30.68 -98.27 REMARK 500 8 LYS A 140 -77.30 -83.46 REMARK 500 8 ASP A 141 -42.09 -168.64 REMARK 500 8 ARG A 144 -59.68 -126.18 REMARK 500 8 CYS A 149 -168.58 -72.71 REMARK 500 8 ILE A 151 -72.94 -59.73 REMARK 500 9 LEU A 136 42.99 -95.50 REMARK 500 9 ASP A 141 -38.10 -177.53 REMARK 500 9 ARG A 144 33.30 -96.82 REMARK 500 9 LYS A 147 79.52 52.53 REMARK 500 9 LYS A 154 31.66 -143.93 REMARK 500 9 ALA A 158 107.68 -169.93 REMARK 500 9 VAL A 176 178.81 -53.88 REMARK 500 9 LEU A 177 31.09 -98.24 REMARK 500 10 CYS A 132 -68.98 -131.38 REMARK 500 10 VAL A 139 173.60 -52.88 REMARK 500 10 ASP A 141 -40.62 -174.81 REMARK 500 10 HIS A 143 -46.37 -166.15 REMARK 500 11 CYS A 132 -66.68 -158.63 REMARK 500 11 LEU A 136 40.49 -96.56 REMARK 500 11 LYS A 140 -78.34 -120.53 REMARK 500 11 TYR A 142 -66.64 69.09 REMARK 500 11 ARG A 144 37.42 -97.44 REMARK 500 11 LYS A 147 93.92 57.63 REMARK 500 11 VAL A 148 146.30 179.29 REMARK 500 11 GLU A 178 -70.16 -138.16 REMARK 500 11 PHE A 180 34.35 -97.87 REMARK 500 12 CYS A 132 111.99 -167.56 REMARK 500 12 LEU A 136 38.33 -97.55 REMARK 500 12 VAL A 139 176.39 -59.15 REMARK 500 12 LYS A 140 -78.75 -105.68 REMARK 500 12 TYR A 142 -66.51 69.02 REMARK 500 12 ARG A 144 -64.60 -156.53 REMARK 500 12 LYS A 147 79.78 67.46 REMARK 500 12 VAL A 148 149.72 179.07 REMARK 500 12 LYS A 154 34.52 -147.40 REMARK 500 12 SER A 172 170.93 64.17 REMARK 500 12 ARG A 173 159.63 62.09 REMARK 500 12 GLU A 179 25.61 -144.67 REMARK 500 13 CYS A 132 -67.03 -153.49 REMARK 500 13 VAL A 139 -179.56 -59.66 REMARK 500 13 LYS A 140 -78.16 -128.28 REMARK 500 13 HIS A 143 -48.10 -165.91 REMARK 500 13 LYS A 147 78.87 61.99 REMARK 500 13 VAL A 148 141.24 -178.90 REMARK 500 13 CYS A 149 -166.07 -74.46 REMARK 500 13 ILE A 151 -72.17 -60.05 REMARK 500 13 LYS A 154 30.90 -147.72 REMARK 500 13 ALA A 158 -169.72 -101.97 REMARK 500 13 GLN A 165 -177.81 -170.38 REMARK 500 13 SER A 172 159.18 63.74 REMARK 500 13 ARG A 173 160.55 61.33 REMARK 500 13 LEU A 177 88.12 -63.09 REMARK 500 13 GLU A 179 31.34 -157.06 REMARK 500 14 ASP A 130 -77.47 -55.21 REMARK 500 14 CYS A 132 100.47 -172.49 REMARK 500 14 LYS A 140 -78.31 -78.75 REMARK 500 14 ASP A 141 -42.05 -168.04 REMARK 500 14 HIS A 143 -41.80 -174.37 REMARK 500 14 ILE A 151 -72.20 -59.65 REMARK 500 14 GLN A 170 -75.47 -59.65 REMARK 500 14 PHE A 174 96.89 -68.90 REMARK 500 14 VAL A 176 176.38 -51.74 REMARK 500 14 LEU A 177 31.29 -97.96 REMARK 500 14 GLU A 179 -44.74 -164.79 REMARK 500 15 LEU A 136 41.78 -96.39 REMARK 500 15 VAL A 139 173.15 -58.96 REMARK 500 15 LYS A 140 -77.19 -111.59 REMARK 500 15 TYR A 142 -66.00 69.33 REMARK 500 15 ARG A 144 -56.98 -150.54 REMARK 500 15 LYS A 147 80.49 64.60 REMARK 500 15 VAL A 148 124.59 -179.57 REMARK 500 15 CYS A 149 -166.43 -58.41 REMARK 500 15 ILE A 151 -70.32 -61.58 REMARK 500 15 SER A 172 165.95 60.85 REMARK 500 15 ARG A 173 150.85 62.18 REMARK 500 15 VAL A 176 -178.77 -52.66 REMARK 500 15 LEU A 177 38.93 -91.09 REMARK 500 15 GLU A 179 31.27 -98.09 REMARK 500 16 CYS A 132 -66.87 -155.84 REMARK 500 16 LYS A 138 34.78 -98.00 REMARK 500 16 LYS A 140 -69.49 -95.09 REMARK 500 16 ASP A 141 -38.69 -174.18 REMARK 500 16 LYS A 147 71.28 65.71 REMARK 500 16 VAL A 148 155.26 179.17 REMARK 500 16 GLN A 169 -75.85 65.35 REMARK 500 16 SER A 172 165.54 65.64 REMARK 500 16 ARG A 173 144.40 63.27 REMARK 500 16 GLU A 178 -49.09 -147.89 REMARK 500 17 GLN A 128 34.24 -96.60 REMARK 500 17 LEU A 136 47.90 -92.69 REMARK 500 17 LYS A 138 35.06 -95.46 REMARK 500 17 ASP A 141 -178.08 -177.54 REMARK 500 17 HIS A 143 -49.24 -161.86 REMARK 500 17 LYS A 147 78.37 65.68 REMARK 500 17 VAL A 148 135.65 -174.80 REMARK 500 17 CYS A 149 -169.51 -73.91 REMARK 500 17 SER A 172 163.30 65.87 REMARK 500 17 ARG A 173 166.01 62.00 REMARK 500 17 GLU A 178 78.61 -172.60 REMARK 500 18 ASP A 130 -76.92 -56.33 REMARK 500 18 ASN A 131 67.02 -69.41 REMARK 500 18 CYS A 132 103.98 -171.13 REMARK 500 18 LYS A 140 -76.95 -101.46 REMARK 500 18 TYR A 142 -66.89 69.08 REMARK 500 18 ILE A 151 -70.35 -64.12 REMARK 500 18 VAL A 176 178.37 -50.76 REMARK 500 18 LEU A 177 44.23 -93.62 REMARK 500 19 ASP A 130 -75.12 -54.85 REMARK 500 19 ASN A 131 65.96 -69.79 REMARK 500 19 LYS A 140 -77.83 -115.17 REMARK 500 19 HIS A 143 -44.55 -164.17 REMARK 500 19 LYS A 147 80.72 62.92 REMARK 500 19 VAL A 148 130.28 -179.84 REMARK 500 19 CYS A 149 -172.13 -67.82 REMARK 500 19 ILE A 151 -67.08 -104.11 REMARK 500 19 HIS A 175 41.01 -164.03 REMARK 500 19 VAL A 176 155.12 61.00 REMARK 500 19 GLU A 178 40.07 -96.27 REMARK 500 19 GLU A 179 70.57 58.51 REMARK 500 20 LEU A 136 58.28 -99.53 REMARK 500 20 VAL A 139 179.56 -56.39 REMARK 500 20 LYS A 140 -75.80 -96.12 REMARK 500 20 ASP A 141 -43.62 -157.95 REMARK 500 20 HIS A 143 40.23 -106.09 REMARK 500 20 ARG A 144 -48.86 -142.87 REMARK 500 20 THR A 157 135.49 -179.06 REMARK 500 20 SER A 172 167.31 61.10 REMARK 500 20 ARG A 173 158.01 60.73 REMARK 500 20 VAL A 176 164.71 -49.59 REMARK 500 20 LEU A 177 37.62 -96.77 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 182 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 132 SG REMARK 620 2 CYS A 127 SG 107.2 REMARK 620 3 CYS A 149 SG 111.4 111.3 REMARK 620 4 HIS A 152 ND1 108.4 112.2 106.4 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 182
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: ATR001004282.1 RELATED DB: TARGETDB
DBREF 1WJ0 A 124 181 UNP Q9S7P5 SPL12_ARATH 124 181
SEQADV 1WJ0 GLY A 122 UNP Q9S7P5 CLONING ARTIFACT SEQADV 1WJ0 SER A 123 UNP Q9S7P5 CLONING ARTIFACT
SEQRES 1 A 60 GLY SER ALA ILE CYS CYS GLN VAL ASP ASN CYS GLY ALA SEQRES 2 A 60 ASP LEU SER LYS VAL LYS ASP TYR HIS ARG ARG HIS LYS SEQRES 3 A 60 VAL CYS GLU ILE HIS SER LYS ALA THR THR ALA LEU VAL SEQRES 4 A 60 GLY GLY ILE MET GLN ARG PHE CYS GLN GLN CYS SER ARG SEQRES 5 A 60 PHE HIS VAL LEU GLU GLU PHE ASP
HET ZN A 182 1
HETNAM ZN ZINC ION
FORMUL 2 ZN ZN 2+
HELIX 1 1 CYS A 149 LYS A 154 1 6
SHEET 1 A 2 ILE A 125 CYS A 126 0 SHEET 2 A 2 ASP A 135 LEU A 136 -1 O LEU A 136 N ILE A 125 SHEET 1 B 2 ALA A 158 VAL A 160 0 SHEET 2 B 2 ILE A 163 GLN A 165 -1 O GLN A 165 N ALA A 158
LINK ZN ZN A 182 SG CYS A 132 1555 1555 2.47 LINK ZN ZN A 182 SG CYS A 127 1555 1555 2.47 LINK ZN ZN A 182 SG CYS A 149 1555 1555 2.47 LINK ZN ZN A 182 ND1 HIS A 152 1555 1555 2.14
SITE 1 AC1 4 CYS A 127 CYS A 132 CYS A 149 HIS A 152
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