HEADER CHAPERONE 05-MAY-19 6K03 TITLE CRYSTAL STRUCTURE OF CEH2A-H2B COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H2B 1,HISTONE H2A; COMPND 3 CHAIN: D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: K-12 KEYWDS H2A-H2B, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR Y.R.LIU REVDAT 2 22-NOV-23 6K03 1 REMARK REVDAT 1 09-OCT-19 6K03 0 JRNL AUTH Y.R.LIU JRNL TITL CRYSTAL STRUCTURE OF XLH2A-H2B JRNL REF STRUCTURE 2019 JRNL REFN ISSN 0969-2126 REMARK 2 REMARK 2 RESOLUTION. 2.86 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 3959 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.180 REMARK 3 FREE R VALUE TEST SET COUNT : 403 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 43.3988 - 4.1196 0.97 1211 149 0.2056 0.2437 REMARK 3 2 4.1196 - 3.2702 0.98 1177 135 0.2321 0.3154 REMARK 3 3 3.2702 - 2.8569 0.97 1168 119 0.3025 0.3677 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) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.62 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 30 THROUGH 212) REMARK 3 ORIGIN FOR THE GROUP (A): -19.7115 13.1587 1.9542 REMARK 3 T TENSOR REMARK 3 T11: 0.3384 T22: 0.3492 REMARK 3 T33: 0.3474 T12: -0.0060 REMARK 3 T13: -0.0130 T23: 0.0015 REMARK 3 L TENSOR REMARK 3 L11: 2.3239 L22: 1.3060 REMARK 3 L33: 2.1932 L12: -0.0593 REMARK 3 L13: -0.7940 L23: 0.3684 REMARK 3 S TENSOR REMARK 3 S11: -0.0072 S12: -0.1981 S13: -0.1744 REMARK 3 S21: 0.0678 S22: -0.0304 S23: 0.0984 REMARK 3 S31: -0.1377 S32: -0.0328 S33: 0.0207 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 6K03 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1300012050. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-19 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 : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3967 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.857 REMARK 200 RESOLUTION RANGE LOW (A) : 44.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.96 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.68000 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: 6K01 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.68800 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.34400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 23.34400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.68800 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: 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 HIS D 28 REMARK 465 MET D 29 REMARK 465 SER D 120 REMARK 465 SER D 121 REMARK 465 LYS D 122 REMARK 465 ALA D 123 REMARK 465 LYS D 124 REMARK 465 THR D 125 REMARK 465 GLY D 126 REMARK 465 GLY D 127 REMARK 465 LYS D 128 REMARK 465 ALA D 129 REMARK 465 LYS D 130 REMARK 465 SER D 131 REMARK 465 ARG D 132 REMARK 465 SER D 133 REMARK 465 SER D 134 REMARK 465 ARG D 135 REMARK 465 ALA D 136 REMARK 465 ALA D 213 REMARK 465 GLY D 214 REMARK 465 VAL D 215 REMARK 465 THR D 216 REMARK 465 ILE D 217 REMARK 465 ALA D 218 REMARK 465 GLN D 219 REMARK 465 GLY D 220 REMARK 465 GLY D 221 REMARK 465 VAL D 222 REMARK 465 LEU D 223 REMARK 465 PRO D 224 REMARK 465 ASN D 225 REMARK 465 ILE D 226 REMARK 465 GLN D 227 REMARK 465 ALA D 228 REMARK 465 VAL D 229 REMARK 465 LEU D 230 REMARK 465 LEU D 231 REMARK 465 PRO D 232 REMARK 465 LYS D 233 REMARK 465 LYS D 234 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG D 30 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 82 CG CD CE NZ REMARK 470 LYS D 151 CG CD CE NZ REMARK 470 GLU D 179 CG CD OE1 OE2 REMARK 470 LYS D 189 CG CD CE NZ 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 SER D 84 2.43 -159.01 REMARK 500 ILE D 98 -53.88 -128.72 REMARK 500 ASN D 153 115.52 -160.48 REMARK 500 REMARK 500 REMARK: NULL DBREF 6K03 D 30 121 UNP P04255 H2B1_CAEEL 30 121 DBREF 6K03 D 122 234 UNP P09588 H2A_CAEEL 9 121 SEQADV 6K03 HIS D 28 UNP P04255 EXPRESSION TAG SEQADV 6K03 MET D 29 UNP P04255 EXPRESSION TAG SEQRES 1 D 207 HIS MET ARG LYS GLU SER TYR SER VAL TYR ILE TYR ARG SEQRES 2 D 207 VAL LEU LYS GLN VAL HIS PRO ASP THR GLY VAL SER SER SEQRES 3 D 207 LYS ALA MET SER ILE MET ASN SER PHE VAL ASN ASP VAL SEQRES 4 D 207 PHE GLU ARG ILE ALA ALA GLU ALA SER ARG LEU ALA HIS SEQRES 5 D 207 TYR ASN LYS ARG SER THR ILE SER SER ARG GLU ILE GLN SEQRES 6 D 207 THR ALA VAL ARG LEU ILE LEU PRO GLY GLU LEU ALA LYS SEQRES 7 D 207 HIS ALA VAL SER GLU GLY THR LYS ALA VAL THR LYS TYR SEQRES 8 D 207 THR SER SER LYS ALA LYS THR GLY GLY LYS ALA LYS SER SEQRES 9 D 207 ARG SER SER ARG ALA GLY LEU GLN PHE PRO VAL GLY ARG SEQRES 10 D 207 LEU HIS ARG ILE LEU ARG LYS GLY ASN TYR ALA GLN ARG SEQRES 11 D 207 VAL GLY ALA GLY ALA PRO VAL TYR LEU ALA ALA VAL LEU SEQRES 12 D 207 GLU TYR LEU ALA ALA GLU VAL LEU GLU LEU ALA GLY ASN SEQRES 13 D 207 ALA ALA ARG ASP ASN LYS LYS THR ARG ILE ALA PRO ARG SEQRES 14 D 207 HIS LEU GLN LEU ALA VAL ARG ASN ASP GLU GLU LEU ASN SEQRES 15 D 207 LYS LEU LEU ALA GLY VAL THR ILE ALA GLN GLY GLY VAL SEQRES 16 D 207 LEU PRO ASN ILE GLN ALA VAL LEU LEU PRO LYS LYS HELIX 1 AA1 TYR D 34 HIS D 46 1 13 HELIX 2 AA2 SER D 52 ASN D 81 1 30 HELIX 3 AA3 SER D 87 LEU D 97 1 11 HELIX 4 AA4 GLY D 101 TYR D 118 1 18 HELIX 5 AA5 PRO D 141 ASN D 153 1 13 HELIX 6 AA6 ALA D 160 ASP D 187 1 28 HELIX 7 AA7 ALA D 194 ASP D 205 1 12 HELIX 8 AA8 ASP D 205 LEU D 212 1 8 SHEET 1 AA1 2 GLY D 50 VAL D 51 0 SHEET 2 AA1 2 ARG D 192 ILE D 193 1 O ILE D 193 N GLY D 50 SHEET 1 AA2 2 THR D 85 ILE D 86 0 SHEET 2 AA2 2 ARG D 157 VAL D 158 1 O ARG D 157 N ILE D 86 CRYST1 63.839 63.839 70.032 90.00 90.00 120.00 P 32 2 1 6 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 0.015664 0.009044 0.000000 0.00000 SCALE2 0.000000 0.018088 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014279 0.00000