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- PDB-5cb3: Structural Insights into the Mechanism of Escherichia coli Ymdb -

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Basic information

Entry
Database: PDB / ID: 5cb3
TitleStructural Insights into the Mechanism of Escherichia coli Ymdb
ComponentsO-acetyl-ADP-ribose deacetylase
KeywordsHYDROLASE / deacetylase / ADPr / OAADPr / macro domain
Function / homology
Function and homology information


O-acetyl-ADP-ribose deacetylase / regulation of single-species biofilm formation on inanimate substrate / O-acetyl-ADP-ribose deacetylase activity / purine nucleoside binding / purine nucleoside metabolic process / endoribonuclease inhibitor activity / response to antibiotic / enzyme binding
Similarity search - Function
O-acetyl-ADP-ribose deacetylase / 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-DIPHOSPHORIBOSE / O-acetyl-ADP-ribose deacetylase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, W. / Wang, C. / Song, Y. / Shao, C. / Zhang, X. / Zang, J.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structural insights into the mechanism of Escherichia coli YmdB: A 2'-O-acetyl-ADP-ribose deacetylase
Authors: Zhang, W. / Wang, C. / Song, Y. / Shao, C. / Zhang, X. / Zang, J.
History
DepositionJun 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-acetyl-ADP-ribose deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2882
Polymers19,7281
Non-polymers5591
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-10 kcal/mol
Surface area7590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.902, 42.059, 70.346
Angle α, β, γ (deg.)90.00, 103.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-591-

HOH

21A-627-

HOH

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Components

#1: Protein O-acetyl-ADP-ribose deacetylase / Regulator of RNase III activity


Mass: 19728.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K12 / Gene: ymdB / Production host: Escherichia coli (E. coli)
References: UniProt: P0A8D6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium sodium tartrate tetrahydrate, 20%(w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 15827 / % possible obs: 99 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 37
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 7.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
Cootmodel building
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SPV

1spv


Resolution: 1.8→29.04 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.666 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21726 791 5 %RANDOM
Rwork0.1878 ---
obs0.1893 15038 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.363 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0 Å2-0.27 Å2
2--0.61 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.8→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1253 0 36 137 1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191317
X-RAY DIFFRACTIONr_bond_other_d0.0050.021222
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9821812
X-RAY DIFFRACTIONr_angle_other_deg0.80732791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2885170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44524.52853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75815177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.921156
X-RAY DIFFRACTIONr_chiral_restr0.0650.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02295
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_it0.9912.539683
X-RAY DIFFRACTIONr_mcbond_other0.9922.535682
X-RAY DIFFRACTIONr_mcangle_it1.7473.8852
X-RAY DIFFRACTIONr_mcangle_other1.7463.805853
X-RAY DIFFRACTIONr_scbond_it1.3122.72634
X-RAY DIFFRACTIONr_scbond_other1.312.719635
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0124.002961
X-RAY DIFFRACTIONr_long_range_B_refined4.26121.4591554
X-RAY DIFFRACTIONr_long_range_B_other3.93120.9271485
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 53 -
Rwork0.237 1118 -
obs--98.57 %

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