HEADER GENE REGULATION 11-MAR-20 6W4L TITLE THE CRYSTAL STRUCTURE OF A SINGLE CHAIN H2B-H2A HISTONE CHIMERA FROM TITLE 2 XENOPUS LAEVIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H2B 1.1,HISTONE H2A TYPE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: H2B1.1; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: SINGLE CHAIN CONSTRUCT LINKING H2B (AA 34-126) AND H2A COMPND 7 (AA 14-105); ONE N-TERMINAL GLY CLONING ARTIFACT.,SINGLE CHAIN COMPND 8 CONSTRUCT LINKING H2B (AA 34-126) AND H2A (AA 14-105); ONE N-TERMINAL COMPND 9 GLY CLONING ARTIFACT. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 4 ORGANISM_TAXID: 8355; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA2; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET30 KEYWDS HISTONE, CHROMATIN, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR C.WARREN,J.B.BONANNO,S.C.ALMO,D.SHECHTER REVDAT 3 18-OCT-23 6W4L 1 REMARK REVDAT 2 13-MAY-20 6W4L 1 JRNL REVDAT 1 06-MAY-20 6W4L 0 JRNL AUTH C.WARREN,J.B.BONANNO,S.C.ALMO,D.SHECHTER JRNL TITL STRUCTURE OF A SINGLE-CHAIN H2A/H2B DIMER. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 76 194 2020 JRNL REFN ESSN 2053-230X JRNL PMID 32356520 JRNL DOI 10.1107/S2053230X20004604 REMARK 2 REMARK 2 RESOLUTION. 1.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0123 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 36283 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1776 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) : 1.32 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.35 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2593 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE SET COUNT : 143 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1375 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 43 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47000 REMARK 3 B22 (A**2) : -0.96000 REMARK 3 B33 (A**2) : 0.33000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.056 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.055 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.749 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1412 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1421 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1909 ; 1.541 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3254 ; 1.057 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 179 ; 4.500 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 59 ;37.634 ;22.203 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 261 ;13.830 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;19.937 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 221 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1570 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 323 ; 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): 2831 ; 1.788 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 22 ;14.972 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2833 ; 5.968 ; 5.000 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 : NULL 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 ANISOTROPICALLY REMARK 4 REMARK 4 6W4L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247598. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97931 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38073 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.310 REMARK 200 RESOLUTION RANGE LOW (A) : 26.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.89200 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: 1KX5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM THIOCYANATE, 20% PEG3350, REMARK 280 PH 6.9, VAPOR DIFFUSION, 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 30.89650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.33950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 30.89650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.33950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1311 LIES ON A SPECIAL POSITION. 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 33 REMARK 465 ARG A 34 REMARK 465 LYS A 35 REMARK 465 GLY A 1099 REMARK 465 GLY A 1100 REMARK 465 VAL A 1101 REMARK 465 THR A 1102 REMARK 465 ILE A 1103 REMARK 465 ALA A 1104 REMARK 465 GLN A 1105 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PPV A 1201 DBREF 6W4L A 34 126 UNP P02281 H2B11_XENLA 34 126 DBREF 6W4L A 1014 1105 UNP P06897 H2A1_XENLA 14 105 SEQADV 6W4L GLY A 33 UNP P02281 EXPRESSION TAG SEQRES 1 A 186 GLY ARG LYS GLU SER TYR ALA ILE TYR VAL TYR LYS VAL SEQRES 2 A 186 LEU LYS GLN VAL HIS PRO ASP THR GLY ILE SER SER LYS SEQRES 3 A 186 ALA MET SER ILE MET ASN SER PHE VAL ASN ASP VAL PHE SEQRES 4 A 186 GLU ARG ILE ALA GLY GLU ALA SER ARG LEU ALA HIS TYR SEQRES 5 A 186 ASN LYS ARG SER THR ILE THR SER ARG GLU ILE GLN THR SEQRES 6 A 186 ALA VAL ARG LEU LEU LEU PRO GLY GLU LEU ALA LYS HIS SEQRES 7 A 186 ALA VAL SER GLU GLY THR LYS ALA VAL THR LYS TYR THR SEQRES 8 A 186 SER ALA LYS LYS ALA LYS THR ARG SER SER ARG ALA GLY SEQRES 9 A 186 LEU GLN PHE PRO VAL GLY ARG VAL HIS ARG LEU LEU ARG SEQRES 10 A 186 LYS GLY ASN TYR ALA GLU ARG VAL GLY ALA GLY ALA PRO SEQRES 11 A 186 VAL TYR LEU ALA ALA VAL LEU GLU TYR LEU THR ALA GLU SEQRES 12 A 186 ILE LEU GLU LEU ALA GLY ASN ALA ALA ARG ASP ASN LYS SEQRES 13 A 186 LYS THR ARG ILE ILE PRO ARG HIS LEU GLN LEU ALA VAL SEQRES 14 A 186 ARG ASN ASP GLU GLU LEU ASN LYS LEU LEU GLY GLY VAL SEQRES 15 A 186 THR ILE ALA GLN HET PPV A1201 9 HETNAM PPV PYROPHOSPHATE FORMUL 2 PPV H4 O7 P2 FORMUL 3 HOH *43(H2 O) HELIX 1 AA1 TYR A 38 HIS A 50 1 13 HELIX 2 AA2 SER A 56 ASN A 85 1 30 HELIX 3 AA3 THR A 91 LEU A 103 1 13 HELIX 4 AA4 PRO A 104 ALA A 125 1 22 HELIX 5 AA5 THR A 1017 ALA A 1022 1 6 HELIX 6 AA6 PRO A 1027 GLY A 1038 1 12 HELIX 7 AA7 ALA A 1046 ASN A 1074 1 29 HELIX 8 AA8 ILE A 1080 ASN A 1090 1 11 HELIX 9 AA9 ASP A 1091 LEU A 1098 1 8 SHEET 1 AA1 2 GLY A 54 ILE A 55 0 SHEET 2 AA1 2 ARG A1078 ILE A1079 1 O ILE A1079 N GLY A 54 SHEET 1 AA2 2 THR A 89 ILE A 90 0 SHEET 2 AA2 2 ARG A1043 VAL A1044 1 O ARG A1043 N ILE A 90 SITE 1 AC1 8 HIS A 50 PRO A 51 ASP A 52 THR A 53 SITE 2 AC1 8 LYS A 121 ARG A1072 HOH A1303 HOH A1316 CRYST1 61.793 44.679 66.450 90.00 117.27 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 0.016183 0.000000 0.008342 0.00000 SCALE2 0.000000 0.022382 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016931 0.00000