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- PDB-5l9q: OCEANOBACILLUS IHEYENSIS MACRODOMAIN WITH ADP -

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Basic information

Entry
Database: PDB / ID: 5l9q
TitleOCEANOBACILLUS IHEYENSIS MACRODOMAIN WITH ADP
ComponentsMACROD-TYPE MACRODOMAIN
KeywordsHYDROLASE / macrodomain / ADP-ribosylation / deacetylase
Function / homology
Function and homology information


O-acetyl-ADP-ribose deacetylase activity / nucleotide binding
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 / Hypothetical conserved protein
Similarity search - Component
Biological speciesOceanobacillus iheyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.3Jan 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
B: MACROD-TYPE MACRODOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6386
Polymers45,5922
Non-polymers1,0474
Water3,351186
1
A: MACROD-TYPE MACRODOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3193
Polymers22,7961
Non-polymers5232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MACROD-TYPE MACRODOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3193
Polymers22,7961
Non-polymers5232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.342, 95.714, 54.734
Angle α, β, γ (deg.)90.00, 115.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A-10 - 500
2111B-10 - 500

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999991, 0.004269, 4.0E-5), (0.004269, -0.999889, -0.014245), (-2.1E-5, 0.014245, -0.999899)-0.06203, 15.5036, -18.32752

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Components

#1: Protein MACROD-TYPE MACRODOMAIN


Mass: 22795.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oceanobacillus iheyensis (strain DSM 14371 / CIP 107618 / JCM 11309 / KCTC 3954 / HTE831) (bacteria)
Gene: OB2288 / Plasmid: pET28a-OiMacroD / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q8EP31
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.76 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M MES pH 6.5, 30% (w/v) PEGMME 5K, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2013 / Details: KB mirrors
RadiationMonochromator: Channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.51
11-H, -K, H+L20.49
ReflectionResolution: 1.75→47.86 Å / Num. obs: 40508 / % possible obs: 91.7 % / Redundancy: 2.2 % / Biso Wilson estimate: 12.42 Å2 / CC1/2: 0.994 / Rsym value: 0.067 / Net I/σ(I): 9.9
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.739 / % possible all: 63

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SPV

1spv


Resolution: 1.75→47.86 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.495 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19833 3203 7.9 %RANDOM
Rwork0.17029 ---
obs0.17247 37246 91.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.392 Å2
Baniso -1Baniso -2Baniso -3
1--8.08 Å2-0 Å2-0.88 Å2
2--13.35 Å20 Å2
3----5.27 Å2
Refinement stepCycle: 1 / Resolution: 1.75→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 64 186 3161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193095
X-RAY DIFFRACTIONr_bond_other_d0.0020.022929
X-RAY DIFFRACTIONr_angle_refined_deg1.5562.014233
X-RAY DIFFRACTIONr_angle_other_deg0.9436743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0695381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36926130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78515512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.112158
X-RAY DIFFRACTIONr_chiral_restr0.0780.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023445
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02663
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0291.8081518
X-RAY DIFFRACTIONr_mcbond_other1.0281.8061517
X-RAY DIFFRACTIONr_mcangle_it1.682.7031895
X-RAY DIFFRACTIONr_mcangle_other1.6792.7051896
X-RAY DIFFRACTIONr_scbond_it1.3722.041577
X-RAY DIFFRACTIONr_scbond_other1.3682.0361570
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2152.9672325
X-RAY DIFFRACTIONr_long_range_B_refined3.73115.0863538
X-RAY DIFFRACTIONr_long_range_B_other3.60814.9393465
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 2855 / Type: tight thermal / Rms dev position: 1.35 Å / Weight position: 0.5
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 175 -
Rwork0.241 1633 -
obs--56.03 %

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