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- PDB-6nsi: Crystal structure of Fe(III)-bound YtgA from Chlamydia trachomatis -

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Basic information

Entry
Database: PDB / ID: 6nsi
TitleCrystal structure of Fe(III)-bound YtgA from Chlamydia trachomatis
ComponentsManganese-binding protein
KeywordsMETAL BINDING PROTEIN / YtgA / solute-binding protein / Chlamydia trachomatis / iron acquisition / ABC transporter
Function / homology
Function and homology information


metal ion transport / periplasmic space / cell adhesion / metal ion binding
Similarity search - Function
Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic
Similarity search - Domain/homology
: / Manganese-binding protein / Metal-binding protein YtgA
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00006345565 Å
AuthorsLuo, Z. / Campbell, R. / Begg, S.L. / Kobe, B. / McDevitt, C.A.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1071659 Australia
National Health and Medical Research Council (NHMRC, Australia)1122582 Australia
Australian Research Council (ARC)DP170102102 Australia
CitationJournal: J.Bacteriol. / Year: 2019
Title: Structure and Metal Binding Properties of Chlamydia trachomatis YtgA.
Authors: Luo, Z. / Neville, S.L. / Campbell, R. / Morey, J.R. / Menon, S. / Thomas, M. / Eijkelkamp, B.A. / Ween, M.P. / Huston, W.M. / Kobe, B. / McDevitt, C.A.
History
DepositionJan 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 30, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Manganese-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8375
Polymers32,6951
Non-polymers1424
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.841, 61.072, 105.500
Angle α, β, γ (deg.)90.000, 96.945, 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-670-

HOH

21A-702-

HOH

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Components

#1: Protein Manganese-binding protein


Mass: 32694.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria)
Gene: troA, troA_1, ERS015772_00125, ERS082928_00414, ERS177788_00539
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E9D6R1, UniProt: Q9S529*PLUS
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 22 % (w/v) polyethylene glycol (PEG) 6000, 0.2 M CaCl2, 0.01 M FeCl3 and 0.1 M MES, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2→19.08 Å / Num. obs: 20476 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 29.9512762463 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.04 / Net I/σ(I): 16.51
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 2001 / CC1/2: 0.734 / Rpim(I) all: 0.39 / % possible all: 98.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
PHENIX1.12_2829refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PSZ

1psz


Resolution: 2.00006345565→19.076725379 Å / SU ML: 0.269741598141 / Cross valid method: FREE R-VALUE / σ(F): 1.38024537978 / Phase error: 25.1403369776
RfactorNum. reflection% reflectionSelection details
Rfree0.225204578609 990 4.83705477109 %random selection
Rwork0.179516182994 ---
obs0.181851425707 20467 99.8438948241 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.1926758415 Å2
Refinement stepCycle: LAST / Resolution: 2.00006345565→19.076725379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2278 0 4 208 2490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008484621793492318
X-RAY DIFFRACTIONf_angle_d0.9416229316743130
X-RAY DIFFRACTIONf_chiral_restr0.063689897835346
X-RAY DIFFRACTIONf_plane_restr0.00506352086264409
X-RAY DIFFRACTIONf_dihedral_angle_d20.6194983044874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.10540.3256500170311410.246821862932742X-RAY DIFFRACTION99.2426850258
2.1054-2.23710.2965501520911260.2191519959132760X-RAY DIFFRACTION100
2.2371-2.40950.2238079944981360.2047775136332813X-RAY DIFFRACTION99.9322263639
2.4095-2.65140.3356425810271320.2125867640682771X-RAY DIFFRACTION100
2.6514-3.03380.2744636416831490.206251749052771X-RAY DIFFRACTION99.8632010944
3.0338-3.81720.2152078455861510.1715121544352782X-RAY DIFFRACTION99.9659168371
3.8172-19.07760.165401807161550.1403282610952838X-RAY DIFFRACTION99.9665998664

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