HEADER DNA BINDING PROTEIN/DNA 11-JUN-22 7Y3L TITLE STRUCTURE OF SALL3 ZFC4 BOUND WITH 12 BP AT-RICH DSDNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SAL-LIKE PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ZINC FINGER PROTEIN 796,ZINC FINGER PROTEIN SALL3,HSALL3; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (12-MER); COMPND 8 CHAIN: G; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (12-MER); COMPND 12 CHAIN: H; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SALL3, ZNF796; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS SALL3, ZINC FINGER, DNA, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR W.RU,C.XU REVDAT 4 29-NOV-23 7Y3L 1 REMARK REVDAT 3 30-NOV-22 7Y3L 1 JRNL REVDAT 2 02-NOV-22 7Y3L 1 JRNL REVDAT 1 26-OCT-22 7Y3L 0 JRNL AUTH W.RU,T.KOGA,X.WANG,Q.GUO,M.D.GEARHART,S.ZHAO,M.MURPHY, JRNL AUTH 2 H.KAWAKAMI,D.CORCORAN,J.ZHANG,Z.ZHU,X.YAO,Y.KAWAKAMI,C.XU JRNL TITL STRUCTURAL STUDIES OF SALL FAMILY PROTEIN ZINC FINGER JRNL TITL 2 CLUSTER DOMAINS IN COMPLEX WITH DNA REVEAL PREFERENTIAL JRNL TITL 3 BINDING TO AN AATA TETRANUCLEOTIDE MOTIF. JRNL REF J.BIOL.CHEM. V. 298 02607 2022 JRNL REFN ESSN 1083-351X JRNL PMID 36257403 JRNL DOI 10.1016/J.JBC.2022.102607 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.RU,T.KOGA,X.WANG,Q.GUO,M.D.GEARHART,S.ZHAO,M.MURPHY, REMARK 1 AUTH 2 H.KAWAKAMI,D.CORCORAN,J.ZHANG,Z.ZHU,X.YAO,Y.KAWAKAMI,C.XU REMARK 1 TITL STRUCTURAL STUDIES OF SALL FAMILY PROTEIN ZINC FINGER REMARK 1 TITL 2 CLUSTER DOMAINS IN COMPLEX WITH DNA REVEAL PREFERENTIAL REMARK 1 TITL 3 BINDING TO AN AATA TETRANUCLEOTIDE MOTIF REMARK 1 REF J.BIOL.CHEM. 2022 REMARK 1 REFN ESSN 1083-351X REMARK 1 DOI DOI.ORG/10.1016/J.JBC.2022.102607 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 5579 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 262 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 37.0560 - 3.1496 0.97 2671 132 0.1985 0.2270 REMARK 3 2 3.1496 - 2.5001 0.98 2646 130 0.2693 0.3548 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.34 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7Y3L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300030195. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5606 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 37.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: 7Y3I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES MONOHYDRATE, PH 6.5, 0.2 M REMARK 280 AMMONIUM SULFATE, 30% W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER REMARK 280 5000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 55.77450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.71100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 55.77450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.71100 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: 2450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, G, H 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 1099 REMARK 465 HIS A 1100 REMARK 465 MET A 1101 REMARK 465 LEU A 1102 REMARK 465 ALA A 1103 REMARK 465 PRO A 1104 REMARK 465 PRO A 1105 REMARK 465 PRO A 1106 REMARK 465 ARG A 1107 REMARK 465 ARG A 1108 REMARK 465 THR A 1109 REMARK 465 PRO A 1110 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 A1201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1115 SG REMARK 620 2 CYS A1118 SG 111.6 REMARK 620 3 HIS A1131 NE2 98.3 98.5 REMARK 620 4 HIS A1135 NE2 102.8 126.7 115.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1143 SG REMARK 620 2 CYS A1146 SG 124.4 REMARK 620 3 HIS A1159 NE2 92.7 110.8 REMARK 620 4 HIS A1163 NE2 108.5 114.2 101.9 REMARK 620 N 1 2 3 DBREF 7Y3L A 1101 1167 UNP Q9BXA9 SALL3_HUMAN 1101 1167 DBREF 7Y3L G 1 12 PDB 7Y3L 7Y3L 1 12 DBREF 7Y3L H 1 12 PDB 7Y3L 7Y3L 1 12 SEQADV 7Y3L GLY A 1099 UNP Q9BXA9 EXPRESSION TAG SEQADV 7Y3L HIS A 1100 UNP Q9BXA9 EXPRESSION TAG SEQRES 1 A 69 GLY HIS MET LEU ALA PRO PRO PRO ARG ARG THR PRO LYS SEQRES 2 A 69 GLN HIS ASN CYS GLN SER CYS GLY LYS THR PHE SER SER SEQRES 3 A 69 ALA SER ALA LEU GLN ILE HIS GLU ARG THR HIS THR GLY SEQRES 4 A 69 GLU LYS PRO PHE GLY CYS THR ILE CYS GLY ARG ALA PHE SEQRES 5 A 69 THR THR LYS GLY ASN LEU LYS VAL HIS MET GLY THR HIS SEQRES 6 A 69 MET TRP ASN ASN SEQRES 1 G 12 DG DG DA DA DA DT DA DT DT DA DC DC SEQRES 1 H 12 DG DG DT DA DA DT DA DT DT DT DC DC HET ZN A1201 1 HET ZN A1202 1 HETNAM ZN ZINC ION FORMUL 4 ZN 2(ZN 2+) FORMUL 6 HOH *36(H2 O) HELIX 1 AA1 SER A 1124 GLY A 1137 1 14 HELIX 2 AA2 THR A 1152 THR A 1162 1 11 SHEET 1 AA1 2 HIS A1113 ASN A1114 0 SHEET 2 AA1 2 THR A1121 PHE A1122 -1 O PHE A1122 N HIS A1113 SHEET 1 AA2 2 PHE A1141 GLY A1142 0 SHEET 2 AA2 2 ALA A1149 PHE A1150 -1 O PHE A1150 N PHE A1141 LINK SG CYS A1115 ZN ZN A1201 1555 1555 2.23 LINK SG CYS A1118 ZN ZN A1201 1555 1555 2.25 LINK NE2 HIS A1131 ZN ZN A1201 1555 1555 2.17 LINK NE2 HIS A1135 ZN ZN A1201 1555 1555 1.84 LINK SG CYS A1143 ZN ZN A1202 1555 1555 2.25 LINK SG CYS A1146 ZN ZN A1202 1555 1555 2.19 LINK NE2 HIS A1159 ZN ZN A1202 1555 1555 1.98 LINK NE2 HIS A1163 ZN ZN A1202 1555 1555 2.15 CRYST1 111.549 39.422 37.986 90.00 103.20 90.00 C 1 2 1 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 0.008965 0.000000 0.002103 0.00000 SCALE2 0.000000 0.025367 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027040 0.00000