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- PDB-8svc: Crystal Structure of SBP from Klebsiella pneumoniae -

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Basic information

Entry
Database: PDB / ID: 8svc
TitleCrystal Structure of SBP from Klebsiella pneumoniae
ComponentsMetal ABC transporter substrate-binding protein
KeywordsMETAL BINDING PROTEIN / periplasmic solute-binding protein
Function / homologyAdhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / metal ion transport / cell adhesion / metal ion binding / Metal ABC transporter substrate-binding protein
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsGiles, M.W. / Cole, G.B. / Ng, D. / McDevitt, C.A. / Moraes, T.F.
Funding support Canada, Australia, 3items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-06546 Canada
Australian Research Council (ARC)DP220100713 Australia
National Health and Medical Research Council (NHMRC, Australia)2010400 Australia
CitationJournal: Front Cell Infect Microbiol / Year: 2023
Title: Zinc acquisition and its contribution to Klebsiella pneumoniae virulence.
Authors: Maunders, E.A. / Giles, M.W. / Ganio, K. / Cunningham, B.A. / Bennett-Wood, V. / Cole, G.B. / Ng, D. / Lai, C.C. / Neville, S.L. / Moraes, T.F. / McDevitt, C.A. / Tan, A.
History
DepositionMay 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2297
Polymers33,6831
Non-polymers5466
Water6,143341
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)62.187, 141.291, 71.388
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-562-

HOH

21A-572-

HOH

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Components

#1: Protein Metal ABC transporter substrate-binding protein


Mass: 33683.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: AJ218 / Gene: EW045_RS05545 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4S7G0W1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium Sulfate and 23% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920099 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920099 Å / Relative weight: 1
ReflectionResolution: 1.59→56.92 Å / Num. obs: 42016 / % possible obs: 98.49 % / Redundancy: 2 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.05254 / Rpim(I) all: 0.05254 / Net I/σ(I): 7.78
Reflection shellResolution: 1.59→1.647 Å / Num. unique obs: 4014 / CC1/2: 0.547

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Processing

Software
NameVersionClassification
autoPROC1.0.5 (20211020)data reduction
PHENIX1.13_2998phasing
PHENIX1.13_2998refinement
Coot1model building
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→56.918 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2102 2084 4.96 %
Rwork0.184 --
obs0.1853 42008 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→56.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1997 0 26 341 2364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062058
X-RAY DIFFRACTIONf_angle_d0.7722796
X-RAY DIFFRACTIONf_dihedral_angle_d2.8881212
X-RAY DIFFRACTIONf_chiral_restr0.049315
X-RAY DIFFRACTIONf_plane_restr0.006358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5901-1.62710.30921280.29722531X-RAY DIFFRACTION95
1.6271-1.66780.29351540.25432580X-RAY DIFFRACTION97
1.6678-1.71290.27571360.2322601X-RAY DIFFRACTION98
1.7129-1.76330.21721420.20812625X-RAY DIFFRACTION99
1.7633-1.82030.25791290.1972643X-RAY DIFFRACTION98
1.8203-1.88530.23381320.18622663X-RAY DIFFRACTION98
1.8853-1.96080.20931360.17282606X-RAY DIFFRACTION98
1.9608-2.05010.19941370.17942652X-RAY DIFFRACTION98
2.0501-2.15810.20731330.17622658X-RAY DIFFRACTION99
2.1581-2.29340.25171300.18542682X-RAY DIFFRACTION99
2.2934-2.47040.24151430.18862662X-RAY DIFFRACTION99
2.4704-2.7190.18421410.1892699X-RAY DIFFRACTION99
2.719-3.11250.2311490.18612712X-RAY DIFFRACTION99
3.1125-3.92120.17281490.16212745X-RAY DIFFRACTION100
3.9212-56.9180.18021450.17222865X-RAY DIFFRACTION100

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