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- PDB-5lbp: Oceanobacillus iheyensis macrodomain mutant N30A -

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Basic information

Entry
Database: PDB / ID: 5lbp
TitleOceanobacillus iheyensis macrodomain mutant N30A
ComponentsMacroD-type macrodomain
KeywordsHYDROLASE / macrodomain / ADP-ribosylation / deacetylase
Function / homology
Function and homology information


Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Hypothetical conserved protein
Similarity search - Component
Biological speciesOceanobacillus iheyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsGil-Ortiz, F. / Zapata-Perez, R. / Martinez, A.B. / Juanhuix, J. / Sanchez-Ferrer, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
MINECO-FEDERBIO2013-45336-R Spain
CitationJournal: Open Biol / Year: 2017
Title: Structural and functional analysis of Oceanobacillus iheyensis macrodomain reveals a network of waters involved in substrate binding and catalysis.
Authors: Zapata-Perez, R. / Gil-Ortiz, F. / Martinez-Monino, A.B. / Garcia-Saura, A.G. / Juanhuix, J. / Sanchez-Ferrer, A.
History
DepositionJun 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MacroD-type macrodomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8482
Polymers22,7531
Non-polymers951
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-7 kcal/mol
Surface area9390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.846, 61.785, 68.806
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MacroD-type macrodomain


Mass: 22752.873 Da / Num. of mol.: 1 / Mutation: N30A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oceanobacillus iheyensis (strain DSM 14371 / JCM 11309 / KCTC 3954 / HTE831) (bacteria)
Gene: OB2288 / Plasmid: pET28A-MacroD / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q8EP31
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.29 Å3/Da / Density % sol: 46 % / Description: Plate
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG1500, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2014 / Details: KB mirrors
RadiationMonochromator: Channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→61.78 Å / Num. obs: 19240 / % possible obs: 99.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 14.342 Å2 / CC1/2: 0.969 / Rsym value: 0.17 / Net I/σ(I): 10.4
Reflection shellResolution: 1.75→1.92 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 3.6 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SPV

1spv


Resolution: 1.76→19.788 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 23.97
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 915 4.91 %Random selection
Rwork0.2048 ---
obs0.2065 18654 97.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.76→19.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1495 0 5 213 1713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091590
X-RAY DIFFRACTIONf_angle_d1.2232169
X-RAY DIFFRACTIONf_dihedral_angle_d15.879585
X-RAY DIFFRACTIONf_chiral_restr0.046255
X-RAY DIFFRACTIONf_plane_restr0.004282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.85280.26671350.20562453X-RAY DIFFRACTION97
1.8528-1.96870.33421160.26552413X-RAY DIFFRACTION95
1.9687-2.12060.27311210.23012523X-RAY DIFFRACTION98
2.1206-2.33370.28391220.24552462X-RAY DIFFRACTION96
2.3337-2.67070.26241400.20992570X-RAY DIFFRACTION100
2.6707-3.36210.22111440.18412607X-RAY DIFFRACTION100
3.3621-19.78930.17421370.1712711X-RAY DIFFRACTION99

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