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- PDB-1hjz: Crystal structure of AF1521 protein containing a macroH2A domain -

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Basic information

Entry
Database: PDB / ID: 1hjz
TitleCrystal structure of AF1521 protein containing a macroH2A domain
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
ADP-ribose glycohydrolase AF_1521
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsAllen, M.D. / Buckle, A.M. / Cordell, S.C. / Lowe, J. / Bycroft, M.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The Crystal Structure of Af1521 a Protein from Archaeoglobus Fulgidus with Homology to the Non-Histone Domain of Macroh2A
Authors: Allen, M.D. / Buckle, A.M. / Cordell, S.C. / Lowe, J. / Bycroft, M.
History
DepositionMar 5, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN AF1521
B: HYPOTHETICAL PROTEIN AF1521
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3574
Polymers41,9662
Non-polymers3902
Water5,026279
1
A: HYPOTHETICAL PROTEIN AF1521
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1782
Polymers20,9831
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HYPOTHETICAL PROTEIN AF1521
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1782
Polymers20,9831
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)119.930, 55.720, 62.740
Angle α, β, γ (deg.)90.00, 115.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HYPOTHETICAL PROTEIN AF1521


Mass: 20983.236 Da / Num. of mol.: 2 / Fragment: MACROH2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Description: SYNTHETIC GENE / Plasmid: MODIFIED PRSET(A) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O28751
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growpH: 6.5
Details: 0.1M MES BUFFER, PH 6.5 18% PEG 5000 MME, 0.2M AMMONIUM SULPHATE, 25MM MANGANESE CHLORIDE
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
118 %(w/v)PEG5000 MME1reservoir
20.1 MMES1reservoirpH6.5
30.2 Mammonium sulfate1reservoir
425 mM1reservoirMnCl2
510 mg/mlprotein1drop
65 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→17.1 Å / Num. obs: 40692 / % possible obs: 98.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 19.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 6.7 / % possible all: 98.5
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 17.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
Mean I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 -5 %RANDOM
Rwork0.203 ---
obs0.203 40692 98.5 %-
Displacement parametersBiso mean: 21.5 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2946 0 24 279 3249
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.185
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 fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2MES.PARMES.TOP
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4WATER.PARAM
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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