HEADER MACRO_H2A DOMAIN/HYDROLASE 10-DEC-04 2BFR TITLE THE MACRO DOMAIN IS AN ADP-RIBOSE BINDING MODULE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN AF1521; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARCHAEOGLOBUS FULGIDUS; SOURCE 3 ORGANISM_TAXID: 2234; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PBE KEYWDS HISTONE MACROH2A, CRYSTAL STRUCTURE P-LOOP, NUCLEOTIDE, HYDROLASE, KEYWDS 2 MACRO_H2A DOMAIN/HYDROLASE, MACRO_H2A DOMAIN-HYDROLASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.I.KARRAS,H.R.BUHECHA,M.D.ALLEN,C.PUGIEUX,F.SAIT,M.BYCROFT, AUTHOR 2 A.G.LADURNER REVDAT 6 20-NOV-24 2BFR 1 REMARK REVDAT 5 13-DEC-23 2BFR 1 REMARK REVDAT 4 10-APR-19 2BFR 1 SOURCE LINK REVDAT 3 24-FEB-09 2BFR 1 VERSN REVDAT 2 21-DEC-06 2BFR 1 JRNL REVDAT 1 16-DEC-04 2BFR 0 JRNL AUTH G.I.KARRAS,G.KUSTATSCHER,H.R.BUHECHA,M.D.ALLEN,C.PUGIEUX, JRNL AUTH 2 F.SAIT,M.BYCROFT,A.G.LADURNER JRNL TITL THE MACRO DOMAIN IS AN ADP-RIBOSE BINDING MODULE. JRNL REF EMBO J. V. 24 1911 2005 JRNL REFN ISSN 0261-4189 JRNL PMID 15902274 JRNL DOI 10.1038/SJ.EMBOJ.7600664 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 9011 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 SET) : 0.202 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 483 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1475 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 40 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.84000 REMARK 3 B22 (A**2) : -0.84000 REMARK 3 B33 (A**2) : 1.68000 REMARK 3 B12 (A**2) : -11.21100 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 0.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 38.59 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : ION.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BFR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1290021917. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93400 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9073 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 28.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.700 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: PDB ENTRY 1HJZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 0.2 MAGNESIUM ACETATE, REMARK 280 0.1M SODIUM CACODYLATE (PH 4.5). 18MG/ML PROTEIN, 1.5MM ADP, 5MM REMARK 280 DTT. CRYOBUFFER CONTAINED 20% GLYCEROL., PH 4.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 20.35633 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 40.71267 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.53450 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 50.89083 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 10.17817 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: PQS 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 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 THR A 22 1.60 -66.02 REMARK 500 MET A 86 -110.56 43.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1194 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A1193 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HJZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AF1521 PROTEIN CONTAINING A MACROH2A DOMAIN REMARK 900 RELATED ID: 1VHU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOESTERASE REMARK 900 RELATED ID: 2BFQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A MACROH2A DOMAIN DBREF 2BFR A 1 192 UNP O28751 YF21_ARCFU 1 192 SEQRES 1 A 192 FME GLU VAL LEU PHE GLU ALA LYS VAL GLY ASP ILE THR SEQRES 2 A 192 LEU LYS LEU ALA GLN GLY ASP ILE THR GLN TYR PRO ALA SEQRES 3 A 192 LYS ALA ILE VAL ASN ALA ALA ASN LYS ARG LEU GLU HIS SEQRES 4 A 192 GLY GLY GLY VAL ALA TYR ALA ILE ALA LYS ALA CYS ALA SEQRES 5 A 192 GLY ASP ALA GLY LEU TYR THR GLU ILE SER LYS LYS ALA SEQRES 6 A 192 MET ARG GLU GLN PHE GLY ARG ASP TYR ILE ASP HIS GLY SEQRES 7 A 192 GLU VAL VAL VAL THR PRO ALA MET ASN LEU GLU GLU ARG SEQRES 8 A 192 GLY ILE LYS TYR VAL PHE HIS THR VAL GLY PRO ILE CYS SEQRES 9 A 192 SER GLY MET TRP SER GLU GLU LEU LYS GLU LYS LEU TYR SEQRES 10 A 192 LYS ALA PHE LEU GLY PRO LEU GLU LYS ALA GLU GLU MET SEQRES 11 A 192 GLY VAL GLU SER ILE ALA PHE PRO ALA VAL SER ALA GLY SEQRES 12 A 192 ILE TYR GLY CYS ASP LEU GLU LYS VAL VAL GLU THR PHE SEQRES 13 A 192 LEU GLU ALA VAL LYS ASN PHE LYS GLY SER ALA VAL LYS SEQRES 14 A 192 GLU VAL ALA LEU VAL ILE TYR ASP ARG LYS SER ALA GLU SEQRES 15 A 192 VAL ALA LEU LYS VAL PHE GLU ARG SER LEU MODRES 2BFR FME A 1 MET N-FORMYLMETHIONINE HET FME A 1 10 HET ADP A1193 27 HET MG A1194 1 HETNAM FME N-FORMYLMETHIONINE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 1 FME C6 H11 N O3 S FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 MG MG 2+ FORMUL 4 HOH *40(H2 O) HELIX 1 1 ASP A 20 TYR A 24 5 5 HELIX 2 2 GLY A 41 GLY A 53 1 13 HELIX 3 3 ASP A 54 GLY A 71 1 18 HELIX 4 4 MET A 86 GLY A 92 5 7 HELIX 5 5 SER A 109 GLY A 131 1 23 HELIX 6 6 ASP A 148 PHE A 163 1 16 HELIX 7 7 ASP A 177 LEU A 192 1 16 SHEET 1 AA 7 GLU A 2 VAL A 9 0 SHEET 2 AA 7 ILE A 12 GLN A 18 -1 O ILE A 12 N VAL A 9 SHEET 3 AA 7 GLU A 170 ILE A 175 1 O VAL A 171 N LYS A 15 SHEET 4 AA 7 SER A 134 PHE A 137 1 O ILE A 135 N ALA A 172 SHEET 5 AA 7 ALA A 28 ALA A 33 1 O ALA A 28 N ALA A 136 SHEET 6 AA 7 TYR A 95 VAL A 100 1 O TYR A 95 N ILE A 29 SHEET 7 AA 7 VAL A 81 PRO A 84 -1 O VAL A 81 N HIS A 98 SSBOND 1 CYS A 104 CYS A 147 1555 1555 2.03 LINK C FME A 1 N GLU A 2 1555 1555 1.33 SITE 1 AC1 1 HIS A 77 SITE 1 AC2 13 ASP A 20 ILE A 21 ALA A 32 GLY A 42 SITE 2 AC2 13 VAL A 43 ALA A 46 ALA A 139 SER A 141 SITE 3 AC2 13 GLY A 143 ILE A 144 TYR A 145 TYR A 176 SITE 4 AC2 13 HOH A2039 CRYST1 87.840 87.840 61.069 90.00 90.00 120.00 P 61 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 0.011384 0.006573 0.000000 0.00000 SCALE2 0.000000 0.013145 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016375 0.00000 HETATM 1 N FME A 1 13.427 83.108 12.836 1.00 44.48 N HETATM 2 CN FME A 1 13.359 84.381 12.494 1.00 48.93 C HETATM 3 O1 FME A 1 14.357 85.107 12.563 1.00 49.65 O HETATM 4 CA FME A 1 12.606 82.010 12.334 1.00 44.86 C HETATM 5 CB FME A 1 13.250 80.665 12.680 1.00 44.26 C HETATM 6 CG FME A 1 12.505 79.452 12.129 1.00 39.61 C HETATM 7 SD FME A 1 12.424 79.457 10.327 1.00 36.11 S HETATM 8 CE FME A 1 14.118 79.021 9.923 1.00 34.05 C HETATM 9 C FME A 1 11.216 82.086 12.950 1.00 45.25 C HETATM 10 O FME A 1 11.063 81.978 14.165 1.00 46.99 O