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- PDB-4wk3: Structure of Staphyloccus aureus PstA -

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Basic information

Entry
Database: PDB / ID: 4wk3
TitleStructure of Staphyloccus aureus PstA
ComponentsPstA
KeywordsSIGNALING PROTEIN / PII
Function / homology
Function and homology information


Cyclic-di-AMP receptor / Cyclic-di-AMP receptor / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein from nitrogen regulatory protein P-II (GLNB) family / Uncharacterized protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMueller, M. / Hopfner, K.-P. / Witte, G.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation3717/2-1 Germany
German Research FoundationGRK1721 Germany
CitationJournal: Febs Lett. / Year: 2015
Title: c-di-AMP recognition by Staphylococcus aureus PstA.
Authors: Muller, M. / Hopfner, K. / Witte, G.
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Dec 31, 2014Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PstA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0532
Polymers14,0181
Non-polymers351
Water724
1
A: PstA
hetero molecules

A: PstA
hetero molecules

A: PstA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1606
Polymers42,0533
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_456z-1,x,y+11
crystal symmetry operation9_546y,z-1,x+11
Buried area4630 Å2
ΔGint-61 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.320, 99.320, 99.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein PstA


Mass: 14017.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q5HIJ4, UniProt: A0A0H2WXZ7*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 55% v/v MPD, 0.1 M sodium-acetate pH 4.3, 10 mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.6→70.2 Å / Num. obs: 5565 / % possible obs: 99.9 % / Redundancy: 36.2 % / Net I/σ(I): 33.1
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 36.1 % / Mean I/σ(I) obs: 2.5 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3m05

3m05


Resolution: 2.6→44.417 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2919 562 10.1 %
Rwork0.2516 --
obs0.2555 5563 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→44.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms593 0 1 4 598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009598
X-RAY DIFFRACTIONf_angle_d1.176807
X-RAY DIFFRACTIONf_dihedral_angle_d15.998213
X-RAY DIFFRACTIONf_chiral_restr0.0598
X-RAY DIFFRACTIONf_plane_restr0.004106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5984-2.85990.35091290.27861203X-RAY DIFFRACTION100
2.8599-3.27360.30421470.2641214X-RAY DIFFRACTION100
3.2736-4.12390.3121480.25441233X-RAY DIFFRACTION100
4.1239-44.42370.27381380.24621351X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -0.1327 Å / Origin y: 2.5644 Å / Origin z: 85.7914 Å
111213212223313233
T0.6139 Å2-0.0981 Å2-0.0051 Å2-0.5585 Å20.0087 Å2--0.6556 Å2
L7.2205 °20.4432 °2-1.3905 °2-9.238 °2-1.8055 °2--7.9668 °2
S-0.1582 Å °0.1691 Å °0.674 Å °0.3539 Å °0.0731 Å °-0.9861 Å °-0.881 Å °0.7668 Å °0.0447 Å °
Refinement TLS groupSelection details: chain A

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