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- PDB-5kiv: Crystal structure of SauMacro (SAV0325) -

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Basic information

Entry
Database: PDB / ID: 5kiv
TitleCrystal structure of SauMacro (SAV0325)
ComponentsProtein-ADP-ribose hydrolase
KeywordsHYDROLASE / Macrodomain / Zn binding / lipoate binding / ADP-ribose
Function / homologyHydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity, acting on glycosyl bonds / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / ETHANOL / Protein-ADP-ribose hydrolase
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWilliams, R.S. / Appel, C.D. / Feld, G.K. / Wallace, B.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01ES102765 United States
CitationJournal: Protein Sci. / Year: 2016
Title: Structure of the sirtuin-linked macrodomain SAV0325 from Staphylococcus aureus.
Authors: Appel, C.D. / Feld, G.K. / Wallace, B.D. / Williams, R.S.
History
DepositionJun 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-ADP-ribose hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9876
Polymers30,7211
Non-polymers2665
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.823, 47.853, 134.950
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 Protein-ADP-ribose hydrolase


Mass: 30721.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P67344, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: SauMacro (25 mg/mL protein plus 1 mM ADP-ribose) with 0.1 M CHES pH 9.5, 15% (v/v) ethanol in a 1:1 ratio (250 nL : 250 nL)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 31085 / % possible obs: 98.83 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.3
Reflection shellHighest resolution: 1.75 Å / Rmerge(I) obs: 0.345 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SPV

1spv


Resolution: 1.75→29.982 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.39
RfactorNum. reflection% reflection
Rfree0.1938 1547 4.99 %
Rwork0.1566 --
obs0.1584 30992 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→29.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 14 307 2374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082125
X-RAY DIFFRACTIONf_angle_d1.0152874
X-RAY DIFFRACTIONf_dihedral_angle_d12.323798
X-RAY DIFFRACTIONf_chiral_restr0.039328
X-RAY DIFFRACTIONf_plane_restr0.005374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80650.26441150.20572412X-RAY DIFFRACTION89
1.8065-1.8710.22391420.19432621X-RAY DIFFRACTION99
1.871-1.94590.3021420.24682625X-RAY DIFFRACTION98
1.9459-2.03450.21321520.16622668X-RAY DIFFRACTION100
2.0345-2.14170.22691610.14952651X-RAY DIFFRACTION100
2.1417-2.27590.18341460.16942665X-RAY DIFFRACTION99
2.2759-2.45150.20461420.14612684X-RAY DIFFRACTION100
2.4515-2.69810.16341120.1392742X-RAY DIFFRACTION100
2.6981-3.08820.21151460.14722729X-RAY DIFFRACTION100
3.0882-3.88940.16731420.14422769X-RAY DIFFRACTION100
3.8894-29.98620.17251470.15082879X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 9.6892 Å / Origin y: -5.5255 Å / Origin z: -11.07 Å
111213212223313233
T0.1429 Å2-0.0102 Å2-0.009 Å2-0.142 Å20.0394 Å2--0.1426 Å2
L1.6606 °2-0.2011 °20.0339 °2-0.7255 °20.0055 °2--0.8559 °2
S0.0007 Å °0.302 Å °0.1366 Å °-0.0891 Å °-0.0312 Å °-0.021 Å °-0.0444 Å °0.0233 Å °-0.007 Å °
Refinement TLS groupSelection details: all

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