HEADER GENE REGULATION/DNA 08-DEC-25 21CH TITLE CRYSTAL STRUCTURE OF SOLANUM LYCOPERSICUM CNR SBP DOMAIN IN COMPLEX TITLE 2 WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SQUAMOSA PROMOTER-BINDING-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*TP*GP*TP*GP*TP*AP*CP*GP*GP*TP*T)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(*AP*AP*CP*CP*GP*TP*AP*CP*AP*CP*A)-3'); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SOLANUM LYCOPERSICUM; SOURCE 3 ORGANISM_COMMON: TOMATO; SOURCE 4 ORGANISM_TAXID: 4081; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-SUMO; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SOLANUM LYCOPERSICUM; SOURCE 12 ORGANISM_TAXID: 4081; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SOLANUM LYCOPERSICUM; SOURCE 16 ORGANISM_TAXID: 4081 KEYWDS SOLANUM LYCOPERSICUM, CNR, SBP, DNA BINDING, TRANSCRIPTION FACTOR, KEYWDS 2 GENE REGULATION/DNA, GENE REGULATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.HE,J.DU REVDAT 1 26-AUG-26 21CH 0 JRNL AUTH Z.ZENG,Y.MA,H.HE,L.LI,Y.PENG,Y.HOU,S.CHAI,P.WANG,C.G.DUAN, JRNL AUTH 2 J.K.ZHU,J.DU,Z.LANG JRNL TITL DNA HYPOMETHYLATION ENABLES THE TRANSCRIPTIONAL REPRESSOR JRNL TITL 2 SLSPL-CNR TO CONTROL FRUIT FLAVOR ESTER BIOSYNTHESIS. JRNL REF NAT COMMUN V. 17 2026 JRNL REFN ESSN 2041-1723 JRNL PMID 42386734 JRNL DOI 10.1038/S41467-026-75181-8 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.780 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 15524 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.190 REMARK 3 FREE R VALUE TEST SET COUNT : 796 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 27.5500 - 4.2300 1.00 2510 139 0.1537 0.1717 REMARK 3 2 4.2300 - 3.3600 0.99 2510 135 0.1688 0.1927 REMARK 3 3 3.3600 - 2.9400 0.99 2485 143 0.2395 0.2883 REMARK 3 4 2.9400 - 2.6700 1.00 2536 140 0.2826 0.2960 REMARK 3 5 2.6700 - 2.4800 1.00 2483 145 0.2740 0.3048 REMARK 3 6 2.4800 - 2.3300 1.00 2520 131 0.2749 0.3212 REMARK 3 7 2.3300 - 2.2100 1.00 2562 122 0.2835 0.3383 REMARK 3 8 2.2100 - 2.1200 1.00 2523 127 0.2879 0.2899 REMARK 3 9 2.1200 - 2.0400 0.99 2513 135 0.3022 0.3333 REMARK 3 10 2.0400 - 1.9700 0.98 2477 153 0.3317 0.3921 REMARK 3 11 1.9700 - 1.9000 0.89 2235 126 0.3519 0.3524 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.016 1181 REMARK 3 ANGLE : 1.663 1677 REMARK 3 CHIRALITY : 0.096 178 REMARK 3 PLANARITY : 0.023 143 REMARK 3 DIHEDRAL : 26.102 480 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 30.7312 24.1380 54.7402 REMARK 3 T TENSOR REMARK 3 T11: 0.4396 T22: 0.3731 REMARK 3 T33: 0.3324 T12: 0.1175 REMARK 3 T13: -0.0351 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 4.3707 L22: 4.8150 REMARK 3 L33: 2.6241 L12: 3.0939 REMARK 3 L13: -1.2838 L23: -0.7769 REMARK 3 S TENSOR REMARK 3 S11: 0.0046 S12: -0.1621 S13: 0.0126 REMARK 3 S21: -0.3086 S22: -0.1429 S23: -0.1196 REMARK 3 S31: 0.2478 S32: 0.4218 S33: 0.1230 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 21CH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 12-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1300057284. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : LN2-COOLED DCM WITH SI(111) REMARK 200 CRYSTALS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15643 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 12.00 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : 0.74600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1WJ0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M TRI-SODIUM CITRATE, 0.1 M SODIUM REMARK 280 HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 25.00700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.09900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.09900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.00700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.55000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 46 REMARK 465 SER A 47 REMARK 465 ALA A 48 REMARK 465 SER A 130 REMARK 465 HIS A 131 REMARK 465 GLY A 132 REMARK 465 GLU A 133 REMARK 465 ASN A 134 REMARK 465 LEU A 135 REMARK 465 GLY A 136 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 ASP A 107 -123.70 52.48 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 52 SG REMARK 620 2 CYS A 57 SG 110.0 REMARK 620 3 CYS A 74 SG 120.1 108.2 REMARK 620 4 HIS A 77 ND1 112.4 104.9 99.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 93 SG REMARK 620 2 CYS A 96 SG 113.3 REMARK 620 3 HIS A 100 NE2 111.2 102.5 REMARK 620 4 CYS A 112 SG 109.0 115.8 104.7 REMARK 620 N 1 2 3 DBREF 21CH A 46 136 UNP Q0PY35 Q0PY35_SOLLC 46 136 DBREF 21CH B 1 11 PDB 21CH 21CH 1 11 DBREF 21CH C 1 11 PDB 21CH 21CH 1 11 SEQRES 1 A 91 GLY SER ALA HIS PRO SER CYS GLN VAL ASP GLN CYS THR SEQRES 2 A 91 ALA ASP MET ALA ASP ALA LYS PRO TYR HIS ARG ARG HIS SEQRES 3 A 91 LYS VAL CYS GLU PHE HIS SER LYS SER PRO ILE VAL LEU SEQRES 4 A 91 ILE SER GLY LEU GLN LYS ARG PHE CYS GLN GLN CYS SER SEQRES 5 A 91 ARG PHE HIS LEU LEU ALA GLU PHE ASP ASP ALA LYS ARG SEQRES 6 A 91 SER CYS ARG ARG ARG LEU ALA GLY HIS ASN GLU ARG ARG SEQRES 7 A 91 ARG LYS ILE THR TYR ASP SER HIS GLY GLU ASN LEU GLY SEQRES 1 B 11 DT DG DT DG DT DA DC DG DG DT DT SEQRES 1 C 11 DA DA DC DC DG DT DA DC DA DC DA HET ZN A 201 1 HET ZN A 202 1 HETNAM ZN ZINC ION FORMUL 4 ZN 2(ZN 2+) FORMUL 6 HOH *45(H2 O) HELIX 1 AA1 ASP A 60 ALA A 64 5 5 HELIX 2 AA2 LYS A 65 HIS A 71 1 7 HELIX 3 AA3 CYS A 74 SER A 80 1 7 HELIX 4 AA4 ALA A 103 PHE A 105 5 3 HELIX 5 AA5 CYS A 112 LYS A 125 1 14 SHEET 1 AA1 3 VAL A 83 ILE A 85 0 SHEET 2 AA1 3 LEU A 88 CYS A 93 -1 O LYS A 90 N VAL A 83 SHEET 3 AA1 3 ARG A 98 LEU A 101 -1 O HIS A 100 N ARG A 91 LINK SG CYS A 52 ZN ZN A 201 1555 1555 2.34 LINK SG CYS A 57 ZN ZN A 201 1555 1555 2.33 LINK SG CYS A 74 ZN ZN A 201 1555 1555 2.31 LINK ND1 HIS A 77 ZN ZN A 201 1555 1555 2.06 LINK SG CYS A 93 ZN ZN A 202 1555 1555 2.29 LINK SG CYS A 96 ZN ZN A 202 1555 1555 2.31 LINK NE2 HIS A 100 ZN ZN A 202 1555 1555 2.00 LINK SG CYS A 112 ZN ZN A 202 1555 1555 2.32 CRYST1 50.014 55.100 70.198 90.00 90.00 90.00 P 21 21 21 4 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 0.019994 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018149 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014245 0.00000 CONECT 29 1118 CONECT 68 1118 CONECT 206 1118 CONECT 233 1118 CONECT 359 1119 CONECT 383 1119 CONECT 421 1119 CONECT 515 1119 CONECT 1118 29 68 206 233 CONECT 1119 359 383 421 515 MASTER 275 0 2 5 3 0 0 6 1161 3 10 9 END