HEADER DNA BINDING PROTEIN 04-JAN-22 7WIN TITLE CRYSTAL STRUCTURE OF BAZ2B TAM DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2B; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HWALP4; COMPND 5 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: BAZ2B, KIAA1476; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS TAM DOMAIN, BAZ2B, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.Y.FENG,K.LIU,J.R.MIN REVDAT 3 29-NOV-23 7WIN 1 REMARK REVDAT 2 17-AUG-22 7WIN 1 JRNL REVDAT 1 02-FEB-22 7WIN 0 JRNL AUTH Y.FENG,S.CHEN,M.ZHOU,J.ZHANG,J.MIN,K.LIU JRNL TITL CRYSTAL STRUCTURE OF THE BAZ2B TAM DOMAIN. JRNL REF HELIYON V. 8 09873 2022 JRNL REFN ESSN 2405-8440 JRNL PMID 35865993 JRNL DOI 10.1016/J.HELIYON.2022.E09873 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 13207 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 666 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 867 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.24 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1694 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 44 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.94000 REMARK 3 B22 (A**2) : 1.43000 REMARK 3 B33 (A**2) : -0.42000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.26000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.211 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.179 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.134 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.718 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1731 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1659 ; 0.001 ; 0.014 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2320 ; 1.598 ; 1.661 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3795 ; 1.274 ; 1.591 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 202 ; 6.446 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 123 ;29.205 ;19.268 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 319 ;17.326 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;22.672 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 202 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1963 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 471 ; 0.001 ; 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): NULL ; NULL ; NULL 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 7WIN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1300026768. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541870 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 5.8.0267 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 3.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13884 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 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 (%) : 97.1 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.3800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 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: MOLREP REMARK 200 STARTING MODEL: 7MWL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% W/V PEG 400, 0.2 M SODIUM CITRATE REMARK 280 TRIBASIC DIHYDRATE, AND 0.1 M TRIS PH 8.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K 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 26.93000 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 735 REMARK 465 ARG A 736 REMARK 465 ARG A 737 REMARK 465 ARG A 738 REMARK 465 VAL A 739 REMARK 465 THR A 740 REMARK 465 ASP A 741 REMARK 465 GLU A 742 REMARK 465 ARG A 844 REMARK 465 ARG A 845 REMARK 465 GLY A 846 REMARK 465 GLY B 735 REMARK 465 ARG B 736 REMARK 465 ARG B 737 REMARK 465 ARG B 738 REMARK 465 VAL B 739 REMARK 465 THR B 740 REMARK 465 ASP B 741 REMARK 465 ARG B 845 REMARK 465 GLY B 846 DBREF 7WIN A 736 846 UNP Q9UIF8 BAZ2B_HUMAN 736 846 DBREF 7WIN B 736 846 UNP Q9UIF8 BAZ2B_HUMAN 736 846 SEQADV 7WIN GLY A 735 UNP Q9UIF8 EXPRESSION TAG SEQADV 7WIN GLY B 735 UNP Q9UIF8 EXPRESSION TAG SEQRES 1 A 112 GLY ARG ARG ARG VAL THR ASP GLU ARG GLU LEU ARG ILE SEQRES 2 A 112 PRO LEU GLU TYR GLY TRP GLN ARG GLU THR ARG ILE ARG SEQRES 3 A 112 ASN PHE GLY GLY ARG LEU GLN GLY GLU VAL ALA TYR TYR SEQRES 4 A 112 ALA PRO CYS GLY LYS LYS LEU ARG GLN TYR PRO GLU VAL SEQRES 5 A 112 ILE LYS TYR LEU SER ARG ASN GLY ILE MET ASP ILE SER SEQRES 6 A 112 ARG ASP ASN PHE SER PHE SER ALA LYS ILE ARG VAL GLY SEQRES 7 A 112 ASP PHE TYR GLU ALA ARG ASP GLY PRO GLN GLY MET GLN SEQRES 8 A 112 TRP CYS LEU LEU LYS GLU GLU ASP VAL ILE PRO ARG ILE SEQRES 9 A 112 ARG ALA MET GLU GLY ARG ARG GLY SEQRES 1 B 112 GLY ARG ARG ARG VAL THR ASP GLU ARG GLU LEU ARG ILE SEQRES 2 B 112 PRO LEU GLU TYR GLY TRP GLN ARG GLU THR ARG ILE ARG SEQRES 3 B 112 ASN PHE GLY GLY ARG LEU GLN GLY GLU VAL ALA TYR TYR SEQRES 4 B 112 ALA PRO CYS GLY LYS LYS LEU ARG GLN TYR PRO GLU VAL SEQRES 5 B 112 ILE LYS TYR LEU SER ARG ASN GLY ILE MET ASP ILE SER SEQRES 6 B 112 ARG ASP ASN PHE SER PHE SER ALA LYS ILE ARG VAL GLY SEQRES 7 B 112 ASP PHE TYR GLU ALA ARG ASP GLY PRO GLN GLY MET GLN SEQRES 8 B 112 TRP CYS LEU LEU LYS GLU GLU ASP VAL ILE PRO ARG ILE SEQRES 9 B 112 ARG ALA MET GLU GLY ARG ARG GLY FORMUL 3 HOH *44(H2 O) HELIX 1 AA1 ARG A 746 TYR A 751 1 6 HELIX 2 AA2 GLN A 782 ASN A 793 1 12 HELIX 3 AA3 SER A 799 PHE A 803 5 5 HELIX 4 AA4 LYS A 830 GLU A 832 5 3 HELIX 5 AA5 ASP A 833 GLY A 843 1 11 HELIX 6 AA6 ARG B 743 TYR B 751 1 9 HELIX 7 AA7 GLN B 782 ASN B 793 1 12 HELIX 8 AA8 SER B 799 PHE B 803 5 5 HELIX 9 AA9 LYS B 830 GLU B 842 1 13 SHEET 1 AA1 5 LYS A 779 LEU A 780 0 SHEET 2 AA1 5 ARG A 765 TYR A 773 -1 N TYR A 772 O LEU A 780 SHEET 3 AA1 5 GLN A 754 PHE A 762 -1 N ARG A 758 O GLU A 769 SHEET 4 AA1 5 ASP A 813 ARG A 818 1 O TYR A 815 N ILE A 759 SHEET 5 AA1 5 GLN A 825 LEU A 828 -1 O GLN A 825 N ARG A 818 SHEET 1 AA2 5 LYS B 779 LEU B 780 0 SHEET 2 AA2 5 ARG B 765 TYR B 773 -1 N TYR B 772 O LEU B 780 SHEET 3 AA2 5 GLN B 754 PHE B 762 -1 N ARG B 760 O GLN B 767 SHEET 4 AA2 5 ASP B 813 ARG B 818 1 O TYR B 815 N ILE B 759 SHEET 5 AA2 5 GLN B 825 LEU B 828 -1 O CYS B 827 N GLU B 816 SSBOND 1 CYS A 827 CYS B 827 1555 1555 2.07 CRYST1 41.344 53.860 44.510 90.00 96.78 90.00 P 1 21 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 0.024187 0.000000 0.002875 0.00000 SCALE2 0.000000 0.018567 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022625 0.00000