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- PDB-6csl: Pneumococcal PhtD protein 269-339 fragment with bound Zn(II) -

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Basic information

Entry
Database: PDB / ID: 6csl
TitlePneumococcal PhtD protein 269-339 fragment with bound Zn(II)
ComponentsHistidine triad protein D
KeywordsMETAL BINDING PROTEIN / polyhistidine triad / zinc homeostasis
Function / homologyStreptococcal histidine triad repeat / Histidine triad protein / PhtA domain superfamily / Streptococcal histidine triad protein / Histidine triad protein D / Pneumococcal histidine triad protein D
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.921 Å
AuthorsLuo, Z. / Pederick, V.G. / Paton, J.C. / McDevitt, C.A. / Kobe, B.
Funding support Australia, 5items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1071659 Australia
National Health and Medical Research Council (NHMRC, Australia)1080784 Australia
National Health and Medical Research Council (NHMRC, Australia)1122582 Australia
Australian Research Council (ARC)DP150104515 Australia
Australian Research Council (ARC)DP170102102 Australia
CitationJournal: FEBS Lett. / Year: 2018
Title: Structural characterisation of the HT3 motif of the polyhistidine triad protein D from Streptococcus pneumoniae.
Authors: Luo, Z. / Pederick, V.G. / Paton, J.C. / McDevitt, C.A. / Kobe, B.
History
DepositionMar 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine triad protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0122
Polymers7,9471
Non-polymers651
Water1,15364
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.034, 47.978, 23.595
Angle α, β, γ (deg.)90.000, 107.130, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-542-

HOH

21A-544-

HOH

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Components

#1: Protein Histidine triad protein D


Mass: 7946.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: phtD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0E3JFJ6, UniProt: Q8DQ08*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium malonate, JED 2003, HEPES, alpha-chymotrypsin

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.25 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
ReflectionResolution: 1.92→18.27 Å / Num. obs: 4744 / % possible obs: 97.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 15.54 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.029 / Rrim(I) all: 0.055 / Net I/σ(I): 25.9 / Num. measured all: 17100
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.92-1.972.80.1367662750.9740.0950.1678.284.5
9.01-18.273.30.039159480.9970.0250.04749.189.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.921→18.274 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 19.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1978 456 9.61 %
Rwork0.1484 4287 -
obs0.1531 4743 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.09 Å2 / Biso mean: 18.2547 Å2 / Biso min: 5.69 Å2
Refinement stepCycle: final / Resolution: 1.921→18.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms561 0 1 64 626
Biso mean--14.27 25.05 -
Num. residues----71
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002582
X-RAY DIFFRACTIONf_angle_d0.563793
X-RAY DIFFRACTIONf_chiral_restr0.04188
X-RAY DIFFRACTIONf_plane_restr0.004105
X-RAY DIFFRACTIONf_dihedral_angle_d12.49355
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9214-2.19910.21071610.1431360152195
2.1991-2.76910.23781380.161514611599100
2.7691-18.2750.17421570.14321466162399

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