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- PDB-7lm5: Crystal structure of the Zn(II)-bound AdcAII H65A mutant variant ... -

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Basic information

Entry
Database: PDB / ID: 7lm5
TitleCrystal structure of the Zn(II)-bound AdcAII H65A 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: 2.4 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)33,46415
Polymers32,6511
Non-polymers81314
Water1,08160
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)46.229, 71.979, 81.914
Angle α, β, γ (deg.)90.000, 95.449, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-402-

ZN

21A-414-

NA

31A-560-

HOH

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Components

#1: Protein Adhesion protein


Mass: 32650.613 Da / Num. of mol.: 1 / Mutation: H65A
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.: 11 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
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: 2.27 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M imidazole pH 8.0, 0.2 M zinc acetate, 20% (w/v) polyethylene glycol 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: May 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.4→36.16 Å / Num. obs: 10512 / % possible obs: 99.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 38.25 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.9
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.298 / Num. unique obs: 1013 / CC1/2: 0.871

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CX3

3cx3


Resolution: 2.4→36.16 Å / SU ML: 0.2167 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.0247 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2686 506 4.82 %
Rwork0.225 10000 -
obs0.2271 10506 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→36.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2103 0 14 60 2177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532141
X-RAY DIFFRACTIONf_angle_d0.61092888
X-RAY DIFFRACTIONf_chiral_restr0.0532326
X-RAY DIFFRACTIONf_plane_restr0.0036370
X-RAY DIFFRACTIONf_dihedral_angle_d16.5378810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.640.29011240.28952461X-RAY DIFFRACTION98.74
2.64-3.020.34321330.28882490X-RAY DIFFRACTION99.85
3.02-3.810.30021190.23792504X-RAY DIFFRACTION99.96
3.81-36.160.21991300.18122545X-RAY DIFFRACTION99.93

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