HEADER DNA BINDING PROTEIN 17-AUG-22 7YUG TITLE STRUCTURE OF HUMAN BANP BEN DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN BANP; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BEN DOMAIN-CONTAINING PROTEIN 1,BTG3-ASSOCIATED NUCLEAR COMPND 5 PROTEIN,SCAFFOLD/MATRIX-ASSOCIATED REGION-1-BINDING PROTEIN; COMPND 6 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: BANP, BEND1, SMAR1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS BANP, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.ZHANG,Y.Q.XIAO,Y.X.CHEN,K.LIU,J.R.MIN REVDAT 4 03-APR-24 7YUG 1 REMARK REVDAT 3 31-MAY-23 7YUG 1 JRNL REVDAT 2 24-MAY-23 7YUG 1 JRNL REVDAT 1 26-APR-23 7YUG 0 JRNL AUTH K.LIU,J.ZHANG,Y.XIAO,A.YANG,X.SONG,Y.LI,Y.CHEN,T.R.HUGHES, JRNL AUTH 2 J.MIN JRNL TITL STRUCTURAL INSIGHTS INTO DNA RECOGNITION BY THE BEN DOMAIN JRNL TITL 2 OF THE TRANSCRIPTION FACTOR BANP. JRNL REF J.BIOL.CHEM. V. 299 04734 2023 JRNL REFN ESSN 1083-351X JRNL PMID 37086783 JRNL DOI 10.1016/J.JBC.2023.104734 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0257 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 42104 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.126 REMARK 3 R VALUE (WORKING SET) : 0.125 REMARK 3 FREE R VALUE : 0.145 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 2348 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.13 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3004 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.1600 REMARK 3 BIN FREE R VALUE SET COUNT : 161 REMARK 3 BIN FREE R VALUE : 0.1870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 953 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 189 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.12000 REMARK 3 B22 (A**2) : 0.39000 REMARK 3 B33 (A**2) : -0.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.027 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.027 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.015 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.660 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.976 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1038 ; 0.019 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 973 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1393 ; 1.867 ; 1.655 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2265 ; 1.609 ; 1.584 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 127 ; 5.760 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 64 ;27.235 ;20.156 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 190 ;11.994 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;14.912 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 130 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1138 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 238 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2011 ;16.162 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7YUG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031227. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JAN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 0.97910 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44514 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 45.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 12.30 REMARK 200 R MERGE FOR SHELL (I) : 0.30700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.920 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: ALPHAFOLD STRUCTURE PREDICTION REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% V/V PEG500*MME;10% W/V PEG REMARK 280 20000,0.09 M HALOGENS, AND 0.1 M TRIS(BASE); BICINE PH 8.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 19.82500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.04600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.02050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.04600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.82500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.02050 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: 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. (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 ARG A 324 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 687 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A 688 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A 689 DISTANCE = 6.36 ANGSTROMS DBREF 7YUG A 208 324 UNP Q8N9N5 BANP_HUMAN 208 324 SEQADV 7YUG GLY A 207 UNP Q8N9N5 EXPRESSION TAG SEQRES 1 A 118 GLY ASN SER GLU GLU ASP TYR PRO ASN GLY THR TRP LEU SEQRES 2 A 118 GLY ASP GLU ASN ASN PRO GLU MET ARG VAL ARG CYS ALA SEQRES 3 A 118 ILE ILE PRO SER ASP MET LEU HIS ILE SER THR ASN CYS SEQRES 4 A 118 ARG THR ALA GLU LYS MET ALA LEU THR LEU LEU ASP TYR SEQRES 5 A 118 LEU PHE HIS ARG GLU VAL GLN ALA VAL SER ASN LEU SER SEQRES 6 A 118 GLY GLN GLY LYS HIS GLY LYS LYS GLN LEU ASP PRO LEU SEQRES 7 A 118 THR ILE TYR GLY ILE ARG CYS HIS LEU PHE TYR LYS PHE SEQRES 8 A 118 GLY ILE THR GLU SER ASP TRP TYR ARG ILE LYS GLN SER SEQRES 9 A 118 ILE ASP SER LYS CYS ARG THR ALA TRP ARG ARG LYS GLN SEQRES 10 A 118 ARG HET PG6 A 401 18 HET PGE A 402 10 HET BR A 403 1 HET CL A 404 1 HET CL A 405 1 HETNAM PG6 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]- HETNAM 2 PG6 ETHOXY}-ETHANE HETNAM PGE TRIETHYLENE GLYCOL HETNAM BR BROMIDE ION HETNAM CL CHLORIDE ION FORMUL 2 PG6 C12 H26 O6 FORMUL 3 PGE C6 H14 O4 FORMUL 4 BR BR 1- FORMUL 5 CL 2(CL 1-) FORMUL 7 HOH *189(H2 O) HELIX 1 AA1 SER A 209 TYR A 213 5 5 HELIX 2 AA2 ILE A 234 CYS A 245 1 12 HELIX 3 AA3 THR A 247 PHE A 260 1 14 HELIX 4 AA4 HIS A 261 VAL A 267 1 7 HELIX 5 AA5 ASP A 282 GLY A 298 1 17 HELIX 6 AA6 THR A 300 LYS A 322 1 23 SHEET 1 AA1 2 THR A 217 GLY A 220 0 SHEET 2 AA1 2 ARG A 228 CYS A 231 -1 O VAL A 229 N LEU A 219 SHEET 1 AA2 2 SER A 268 ASN A 269 0 SHEET 2 AA2 2 LYS A 279 GLN A 280 1 O LYS A 279 N ASN A 269 CRYST1 39.650 50.041 54.092 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 0.025221 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019984 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018487 0.00000