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- PDB-2bfr: The Macro domain is an ADP-ribose binding module -

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Basic information

Entry
Database: PDB / ID: 2bfr
TitleThe Macro domain is an ADP-ribose binding module
ComponentsHYPOTHETICAL PROTEIN AF1521
KeywordsMACRO_H2A DOMAIN/HYDROLASE / HISTONE MACROH2A / CRYSTAL STRUCTURE P-LOOP / NUCLEOTIDE / HYDROLASE / MACRO_H2A DOMAIN-HYDROLASE complex
Function / homology
Function and homology information


ADP-ribosylglutamate hydrolase activity / peptidyl-glutamate ADP-deribosylation / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
Similarity search - Function
Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADP-ribose glycohydrolase AF_1521
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKarras, G.I. / Buhecha, H.R. / Allen, M.D. / Pugieux, C. / Sait, F. / Bycroft, M. / Ladurner, A.G.
CitationJournal: Embo J. / Year: 2005
Title: The Macro Domain is an Adp-Ribose Binding Module.
Authors: Karras, G.I. / Kustatscher, G. / Buhecha, H.R. / Allen, M.D. / Pugieux, C. / Sait, F. / Bycroft, M. / Ladurner, A.G.
History
DepositionDec 10, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 10, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN AF1521
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4633
Polymers21,0111
Non-polymers4522
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.840, 87.840, 61.069
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein HYPOTHETICAL PROTEIN AF1521


Mass: 21011.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Plasmid: PBE / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): C41 / References: UniProt: O28751
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61 %
Crystal growpH: 4.5
Details: 20% PEG 8000, 0.2 MAGNESIUM ACETATE, 0.1M SODIUM CACODYLATE (PH 4.5). 18MG/ML PROTEIN, 1.5MM ADP, 5MM DTT. CRYOBUFFER CONTAINED 20% GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.934
DetectorDate: May 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→28.75 Å / Num. obs: 9073 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.2
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.7 / % possible all: 97.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HJZ

1hjz


Resolution: 2.5→25 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 483 5.2 %RANDOM
Rwork0.202 ---
obs0.202 9011 96.1 %-
Solvent computationBsol: 38.5864 Å2 / ksol: 0.356954 e/Å3
Displacement parametersBiso mean: 34.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-11.211 Å20 Å2
2---0.84 Å20 Å2
3---1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1475 0 28 40 1543
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1ION.PARAM
X-RAY DIFFRACTION2WATER.PARAM

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