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- PDB-4pq1: Crystal structure and functional implications of a DsbF homologue... -

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Basic information

Entry
Database: PDB / ID: 4pq1
TitleCrystal structure and functional implications of a DsbF homologue from Corynebacterium diphtheriae
ComponentsPutative electron transport related protein
KeywordsOXIDOREDUCTASE / Thioredoxin-like region / reductant / oxidant
Function / homology
Function and homology information


antioxidant activity / oxidoreductase activity
Similarity search - Function
: / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Electron transport related protein
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 Å
AuthorsUm, S.H. / Kim, J.S. / Yoon, B.Y. / Ha, N.C.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structure of a DsbF homologue from Corynebacterium diphtheriae.
Authors: Um, S.H. / Kim, J.S. / Lee, K. / Ha, N.C.
History
DepositionFeb 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Putative electron transport related protein
B: Putative electron transport related protein


Theoretical massNumber of molelcules
Total (without water)34,6152
Polymers34,6152
Non-polymers00
Water2,684149
1
A: Putative electron transport related protein


Theoretical massNumber of molelcules
Total (without water)17,3071
Polymers17,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative electron transport related protein


Theoretical massNumber of molelcules
Total (without water)17,3071
Polymers17,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.103, 36.162, 62.522
Angle α, β, γ (deg.)90.00, 67.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative electron transport related protein / DsbF


Mass: 17307.289 Da / Num. of mol.: 2 / Fragment: UNP residues 29-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Strain: NCTC 13129 / Gene: DIP0411 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NJJ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.38 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M tris-HCl, 30% PEG 4K, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 287.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97951 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.097→36.181 Å / Num. all: 19396 / Num. obs: 18081 / % possible obs: 93.22 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.65 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.09-2.2186
2.2-2.34188
2.34-2.5210.91
2.52-2.78193
2.78-3.18196
3.18-4199

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.097→36.181 Å / FOM work R set: 0.8017 / SU ML: 0.27 / σ(F): 1.52 / σ(I): 0 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 914 5.05 %RANDOM
Rwork0.1836 ---
obs0.1868 17168 93.22 %-
all-19396 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.53 Å2 / Biso mean: 34.04 Å2 / Biso min: 14.99 Å2
Refinement stepCycle: LAST / Resolution: 2.097→36.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 0 0 149 2583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082515
X-RAY DIFFRACTIONf_angle_d1.0883426
X-RAY DIFFRACTIONf_chiral_restr0.042383
X-RAY DIFFRACTIONf_plane_restr0.006452
X-RAY DIFFRACTIONf_dihedral_angle_d14.193916
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0967-2.20720.34121130.28272238235186
2.2072-2.34540.30461090.26622310241988
2.3454-2.52650.30691480.23012341248991
2.5265-2.78070.28281320.21762454258693
2.7807-3.18280.23591440.18522487263196
3.1828-4.00920.23061250.15992647277299
4.0092-36.18620.20651430.13852691283499

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