PDB Short entry for 5L7A HEADER DNA BINDING PROTEIN 02-JUN-16 5L7A TITLE THE CRYSTAL STRUCTURE OF THE HUMAN SNF5/INI1 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR COMPND 3 OF CHROMATIN SUBFAMILY B MEMBER 1; COMPND 4 CHAIN: A, B, C, D; COMPND 5 SYNONYM: BRG1-ASSOCIATED FACTOR 47,BAF47,INTEGRASE INTERACTOR 1 COMPND 6 PROTEIN,SNF5 HOMOLOG,HSNF5; COMPND 7 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: SMARCB1, BAF47, INI1, SNF5L1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: C41 KEYWDS SNF5 INI1 DOMAIN CRYSTAL, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.D.ALLEN,G.ZINZALLA,M.BYCROFT REVDAT 6 10-JAN-24 5L7A 1 REMARK REVDAT 5 10-APR-19 5L7A 1 SOURCE REVDAT 4 27-FEB-19 5L7A 1 JRNL REVDAT 3 10-OCT-18 5L7A 1 JRNL REVDAT 2 24-MAY-17 5L7A 1 TITLE REVDAT 1 10-MAY-17 5L7A 0 JRNL AUTH S.SAMMAK,M.D.ALLEN,N.HAMDANI,M.BYCROFT,G.ZINZALLA JRNL TITL THE STRUCTURE OF INI1/HSNF5 RPT1 AND ITS INTERACTIONS WITH JRNL TITL 2 THE C-MYC:MAX HETERODIMER PROVIDE INSIGHTS INTO THE JRNL TITL 3 INTERPLAY BETWEEN MYC AND THE SWI/SNF CHROMATIN REMODELING JRNL TITL 4 COMPLEX. JRNL REF FEBS J. V. 285 4165 2018 JRNL REFN ISSN 1742-4658 JRNL PMID 30222246 JRNL DOI 10.1111/FEBS.14660 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2386: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.290 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.7 REMARK 3 NUMBER OF REFLECTIONS : 15656 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1395 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 21.4202 - 4.5156 0.91 2777 138 0.1657 0.1980 REMARK 3 2 4.5156 - 3.5896 0.89 2730 143 0.1618 0.1983 REMARK 3 3 3.5896 - 3.1375 0.87 2670 138 0.1921 0.3031 REMARK 3 4 3.1375 - 2.8513 0.87 2663 135 0.2157 0.2684 REMARK 3 5 2.8513 - 2.6474 0.85 2635 125 0.2325 0.3241 REMARK 3 6 2.6474 - 2.4915 0.84 2617 121 0.2321 0.2718 REMARK 3 7 2.4915 - 2.3669 0.83 2489 150 0.2324 0.3379 REMARK 3 8 2.3669 - 2.2640 0.81 2504 146 0.2391 0.2798 REMARK 3 9 2.2640 - 2.1769 0.81 2418 147 0.2592 0.3562 REMARK 3 10 2.1769 - 2.1019 0.79 2391 152 0.2933 0.3712 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.770 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 : 0.008 2154 REMARK 3 ANGLE : 0.918 2920 REMARK 3 CHIRALITY : 0.051 337 REMARK 3 PLANARITY : 0.007 380 REMARK 3 DIHEDRAL : 12.252 1338 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 5L7A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1200000245. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54179 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15711 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: 5L7B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M TRI-SODIUM CITRATE AND 100 MM REMARK 280 HEPES PH 7.5, VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 36.82650 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 181 REMARK 465 GLY A 182 REMARK 465 SER A 183 REMARK 465 GLU A 184 REMARK 465 PRO A 249 REMARK 465 THR A 250 REMARK 465 ASP A 251 REMARK 465 SER A 252 REMARK 465 GLY B 181 REMARK 465 GLY B 182 REMARK 465 SER B 183 REMARK 465 GLU B 184 REMARK 465 PRO B 249 REMARK 465 THR B 250 REMARK 465 ASP B 251 REMARK 465 SER B 252 REMARK 465 PRO C 249 REMARK 465 THR C 250 REMARK 465 ASP C 251 REMARK 465 SER C 252 REMARK 465 THR D 250 REMARK 465 ASP D 251 REMARK 465 SER D 252 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 LYS C 211 -52.92 -126.46 REMARK 500 ASP D 192 77.26 -160.03 REMARK 500 REMARK 500 REMARK: NULL DBREF 5L7A A 184 252 UNP Q12824 SNF5_HUMAN 184 252 DBREF 5L7A B 184 252 UNP Q12824 SNF5_HUMAN 184 252 DBREF 5L7A C 184 252 UNP Q12824 SNF5_HUMAN 184 252 DBREF 5L7A D 184 252 UNP Q12824 SNF5_HUMAN 184 252 SEQADV 5L7A GLY A 181 UNP Q12824 EXPRESSION TAG SEQADV 5L7A GLY A 182 UNP Q12824 EXPRESSION TAG SEQADV 5L7A SER A 183 UNP Q12824 EXPRESSION TAG SEQADV 5L7A GLY B 181 UNP Q12824 EXPRESSION TAG SEQADV 5L7A GLY B 182 UNP Q12824 EXPRESSION TAG SEQADV 5L7A SER B 183 UNP Q12824 EXPRESSION TAG SEQADV 5L7A GLY C 181 UNP Q12824 EXPRESSION TAG SEQADV 5L7A GLY C 182 UNP Q12824 EXPRESSION TAG SEQADV 5L7A SER C 183 UNP Q12824 EXPRESSION TAG SEQADV 5L7A GLY D 181 UNP Q12824 EXPRESSION TAG SEQADV 5L7A GLY D 182 UNP Q12824 EXPRESSION TAG SEQADV 5L7A SER D 183 UNP Q12824 EXPRESSION TAG SEQRES 1 A 72 GLY GLY SER GLU VAL LEU VAL PRO ILE ARG LEU ASP MET SEQRES 2 A 72 GLU ILE ASP GLY GLN LYS LEU ARG ASP ALA PHE THR TRP SEQRES 3 A 72 ASN MET ASN GLU LYS LEU MET THR PRO GLU MET PHE SER SEQRES 4 A 72 GLU ILE LEU CYS ASP ASP LEU ASP LEU ASN PRO LEU THR SEQRES 5 A 72 PHE VAL PRO ALA ILE ALA SER ALA ILE ARG GLN GLN ILE SEQRES 6 A 72 GLU SER TYR PRO THR ASP SER SEQRES 1 B 72 GLY GLY SER GLU VAL LEU VAL PRO ILE ARG LEU ASP MET SEQRES 2 B 72 GLU ILE ASP GLY GLN LYS LEU ARG ASP ALA PHE THR TRP SEQRES 3 B 72 ASN MET ASN GLU LYS LEU MET THR PRO GLU MET PHE SER SEQRES 4 B 72 GLU ILE LEU CYS ASP ASP LEU ASP LEU ASN PRO LEU THR SEQRES 5 B 72 PHE VAL PRO ALA ILE ALA SER ALA ILE ARG GLN GLN ILE SEQRES 6 B 72 GLU SER TYR PRO THR ASP SER SEQRES 1 C 72 GLY GLY SER GLU VAL LEU VAL PRO ILE ARG LEU ASP MET SEQRES 2 C 72 GLU ILE ASP GLY GLN LYS LEU ARG ASP ALA PHE THR TRP SEQRES 3 C 72 ASN MET ASN GLU LYS LEU MET THR PRO GLU MET PHE SER SEQRES 4 C 72 GLU ILE LEU CYS ASP ASP LEU ASP LEU ASN PRO LEU THR SEQRES 5 C 72 PHE VAL PRO ALA ILE ALA SER ALA ILE ARG GLN GLN ILE SEQRES 6 C 72 GLU SER TYR PRO THR ASP SER SEQRES 1 D 72 GLY GLY SER GLU VAL LEU VAL PRO ILE ARG LEU ASP MET SEQRES 2 D 72 GLU ILE ASP GLY GLN LYS LEU ARG ASP ALA PHE THR TRP SEQRES 3 D 72 ASN MET ASN GLU LYS LEU MET THR PRO GLU MET PHE SER SEQRES 4 D 72 GLU ILE LEU CYS ASP ASP LEU ASP LEU ASN PRO LEU THR SEQRES 5 D 72 PHE VAL PRO ALA ILE ALA SER ALA ILE ARG GLN GLN ILE SEQRES 6 D 72 GLU SER TYR PRO THR ASP SER FORMUL 5 HOH *130(H2 O) HELIX 1 AA1 THR A 214 LEU A 226 1 13 HELIX 2 AA2 ASN A 229 GLU A 246 1 18 HELIX 3 AA3 THR B 214 ASP B 227 1 14 HELIX 4 AA4 ASN B 229 ILE B 245 1 17 HELIX 5 AA5 GLY C 181 GLU C 184 5 4 HELIX 6 AA6 THR C 214 ASP C 227 1 14 HELIX 7 AA7 ASN C 229 TYR C 248 1 20 HELIX 8 AA8 THR D 214 LEU D 226 1 13 HELIX 9 AA9 ASN D 229 TYR D 248 1 20 SHEET 1 AA1 4 GLN A 198 ASN A 207 0 SHEET 2 AA1 4 LEU A 186 ILE A 195 -1 N MET A 193 O LEU A 200 SHEET 3 AA1 4 LEU D 186 ILE D 195 -1 O GLU D 194 N GLU A 194 SHEET 4 AA1 4 GLN D 198 ASN D 207 -1 O PHE D 204 N ILE D 189 SHEET 1 AA2 4 GLN B 198 ASN B 207 0 SHEET 2 AA2 4 LEU B 186 ILE B 195 -1 N ILE B 189 O PHE B 204 SHEET 3 AA2 4 LEU C 186 ILE C 195 -1 O GLU C 194 N GLU B 194 SHEET 4 AA2 4 GLN C 198 ASN C 207 -1 O LEU C 200 N MET C 193 CRYST1 43.619 73.653 46.460 90.00 106.60 90.00 P 1 21 1 8 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 0.022926 0.000000 0.006833 0.00000 SCALE2 0.000000 0.013577 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022459 0.00000