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- PDB-7lm7: Crystal structure of the Zn(II)-bound AdcAII E280Q mutant variant... -

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Basic information

Entry
Database: PDB / ID: 7lm7
TitleCrystal structure of the Zn(II)-bound AdcAII E280Q mutant variant of Streptococcus pneumoniae
ComponentsAdhesion protein
KeywordsMETAL BINDING PROTEIN / SBP / ATP-binding cassette transporter / Zn acquisition
Function / homologyAdhesin B / Adhesion lipoprotein / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / metal ion transport / Prokaryotic membrane lipoprotein lipid attachment site profile. / cell adhesion / metal ion binding / Adhesion protein
Function and homology information
Biological speciesStreptococcus pseudopneumoniae 5247 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsLuo, Z. / Zupan, M. / McDevitt, C.A. / Kobe, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Front Cell Infect Microbiol / Year: 2021
Title: Conformation of the Solute-Binding Protein AdcAII Influences Zinc Uptake in Streptococcus pneumoniae .
Authors: Zupan, M.L. / Luo, Z. / Ganio, K. / Pederick, V.G. / Neville, S.L. / Deplazes, E. / Kobe, B. / McDevitt, C.A.
History
DepositionFeb 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,40612
Polymers32,7171
Non-polymers69011
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.346, 72.959, 81.463
Angle α, β, γ (deg.)90.00, 95.57, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-402-

ZN

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Components

#1: Protein Adhesion protein


Mass: 32716.699 Da / Num. of mol.: 1 / Mutation: E280Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pseudopneumoniae 5247 (bacteria)
Gene: U753_04975
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: V8IJK5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M imidazole pH 8.0, 0.2 M zinc acetate, 20% (w/v) polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 3.12→39.58 Å / Num. obs: 4870 / % possible obs: 98 % / Redundancy: 4 % / Biso Wilson estimate: 68.51 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.043 / Net I/σ(I): 11.8
Reflection shellResolution: 3.12→3.23 Å / Rmerge(I) obs: 0.19 / Num. unique obs: 412 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CX3

3cx3


Resolution: 3.12→39.58 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2603 218 4.48 %
Rwork0.2185 --
obs0.2203 4870 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.12→39.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 11 0 2144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132173
X-RAY DIFFRACTIONf_angle_d1.272932
X-RAY DIFFRACTIONf_dihedral_angle_d18.392822
X-RAY DIFFRACTIONf_chiral_restr0.081330
X-RAY DIFFRACTIONf_plane_restr0.008376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.12-3.9250.33591030.26152258X-RAY DIFFRACTION96
3.925-39.580.22911150.19762394X-RAY DIFFRACTION100

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