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- PDB-5kbc: Crystal structure of Chlamydia trachomatis DsbA -

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Basic information

Entry
Database: PDB / ID: 5kbc
TitleCrystal structure of Chlamydia trachomatis DsbA
ComponentsDsbA
KeywordsOXIDOREDUCTASE / thioredoxin fold
Function / homologyThioredoxin / Thioredoxin-like fold / Thioredoxin-like superfamily / membrane / DsbA
Function and homology information
Biological speciesChlamydia trachomatis serovar A (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.706 Å
AuthorsMcMahon, R.M. / Groftehauge, M.K. / Martin, J.L.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)FL0992138 Australia
National Health and Medical Research Council (NHMRC, Australia)1061241 Australia
CitationJournal: PLoS ONE / Year: 2016
Title: Structural and Biochemical Characterization of Chlamydia trachomatis DsbA Reveals a Cysteine-Rich and Weakly Oxidising Oxidoreductase.
Authors: Christensen, S. / Grftehauge, M.K. / Byriel, K. / Huston, W.M. / Furlong, E. / Heras, B. / Martin, J.L. / McMahon, R.M.
History
DepositionJun 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DsbA
B: DsbA


Theoretical massNumber of molelcules
Total (without water)45,5682
Polymers45,5682
Non-polymers00
Water39622
1
B: DsbA


Theoretical massNumber of molelcules
Total (without water)22,7841
Polymers22,7841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DsbA


Theoretical massNumber of molelcules
Total (without water)22,7841
Polymers22,7841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.251, 98.131, 44.789
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DsbA


Mass: 22784.164 Da / Num. of mol.: 2 / Fragment: UNP residues 78-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis serovar A (bacteria)
Strain: A2497 / Gene: CTO_0193 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: G4NNC6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 9
Details: 100 mM Bis Tris pH 9.0, 3.1 M sodium formate, 4 % (v/v) Tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.706→43.319 Å / Num. obs: 11646 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Net I/σ(I): 19.6
Reflection shellResolution: 2.706→2.715 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 5.9 / % possible all: 86.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å43.32 Å
Translation3 Å43.32 Å

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
PHASER2.5.0phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EU3

3eu3


Resolution: 2.706→43.319 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2823 554 4.77 %
Rwork0.2476 11056 -
obs0.2492 11610 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.52 Å2 / Biso mean: 50.488 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.706→43.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3082 0 0 22 3104
Biso mean---44.19 -
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033171
X-RAY DIFFRACTIONf_angle_d0.6924311
X-RAY DIFFRACTIONf_chiral_restr0.088487
X-RAY DIFFRACTIONf_plane_restr0.003554
X-RAY DIFFRACTIONf_dihedral_angle_d14.4391180
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7058-2.97810.34741390.29952687282699
2.9781-3.40890.32771250.270827342859100
3.4089-4.29420.241520.235527392891100
4.2942-43.32490.27071380.223728963034100

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