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- PDB-4oxr: Structure of Staphylococcus pseudintermedius metal-binding protei... -

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Basic information

Entry
Database: PDB / ID: 4oxr
TitleStructure of Staphylococcus pseudintermedius metal-binding protein SitA in complex with Manganese
ComponentsManganese ABC transporter, periplasmic-binding protein SitA
KeywordsMETAL BINDING PROTEIN / Manganese binding protein / SBP / ABC transporter
Function / homologyNitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : / :
Function and homology information
Biological speciesStaphylococcus pseudintermedius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAbate, F. / Malito, E. / Bottomley, M.
CitationJournal: Biosci.Rep. / Year: 2014
Title: Apo, Zn2+-bound and Mn2+-bound structures reveal ligand-binding properties of SitA from the pathogen Staphylococcus pseudintermedius.
Authors: Abate, F. / Malito, E. / Cozzi, R. / Lo Surdo, P. / Maione, D. / Bottomley, M.J.
History
DepositionFeb 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Feb 11, 2015Group: Database references
Revision 1.4Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / software / struct_keywords / struct_site / symmetry
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text / _struct_site.details / _symmetry.Int_Tables_number
Revision 1.5Sep 27, 2023Group: 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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Manganese ABC transporter, periplasmic-binding protein SitA
B: Manganese ABC transporter, periplasmic-binding protein SitA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4844
Polymers64,3742
Non-polymers1102
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-5 kcal/mol
Surface area25140 Å2
2
A: Manganese ABC transporter, periplasmic-binding protein SitA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2422
Polymers32,1871
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Manganese ABC transporter, periplasmic-binding protein SitA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2422
Polymers32,1871
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.580, 57.490, 112.349
Angle α, β, γ (deg.)90.00, 101.95, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 29 - 306 / Label seq-ID: 8 - 285

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Manganese ABC transporter, periplasmic-binding protein SitA


Mass: 32187.090 Da / Num. of mol.: 2 / Fragment: ectodomain (UNP residues 23-306)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus pseudintermedius (bacteria)
Strain: IV369-1041 / Gene: SPSE_2131 / Plasmid: pET-15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F0P9H5
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1,1,1,3,3,3-hexafluoro-2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2→46.45 Å / Num. obs: 33582 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 16.69 Å2 / Rsym value: 0.116 / Net I/σ(I): 11.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 4.7 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1593)refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PSZ

1psz


Resolution: 2→39.417 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2332 1701 5.07 %
Rwork0.183 --
obs0.1856 33559 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.8 Å2
Refinement stepCycle: LAST / Resolution: 2→39.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4423 0 2 181 4606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014528
X-RAY DIFFRACTIONf_angle_d1.4536096
X-RAY DIFFRACTIONf_dihedral_angle_d10.8741739
X-RAY DIFFRACTIONf_chiral_restr0.064662
X-RAY DIFFRACTIONf_plane_restr0.009784
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2497X-RAY DIFFRACTION6.633TORSIONAL
12B2497X-RAY DIFFRACTION6.633TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05890.34241460.24052614X-RAY DIFFRACTION97
2.0589-2.12530.2921680.22642599X-RAY DIFFRACTION98
2.1253-2.20130.28711250.21762645X-RAY DIFFRACTION98
2.2013-2.28940.25221490.21182617X-RAY DIFFRACTION98
2.2894-2.39360.26461190.212635X-RAY DIFFRACTION98
2.3936-2.51980.23871290.20472666X-RAY DIFFRACTION98
2.5198-2.67760.2971410.19622646X-RAY DIFFRACTION98
2.6776-2.88430.22231440.18842651X-RAY DIFFRACTION98
2.8843-3.17440.24311430.18962663X-RAY DIFFRACTION99
3.1744-3.63350.2171170.16382717X-RAY DIFFRACTION99

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