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- PDB-1t3b: X-ray Structure of DsbC from Haemophilus influenzae -

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Basic information

Entry
Database: PDB / ID: 1t3b
TitleX-ray Structure of DsbC from Haemophilus influenzae
ComponentsThiol:disulfide interchange protein dsbC
KeywordsISOMERASE / OXIDOREDUCTASE / PROTEIN DISULFIDE ISOMERASE / PROTEIN FOLDING / REDOX PROTEIN / REDOX-ACTIVE CENTER
Function / homology
Function and homology information


Disulphide bond isomerase, DsbC/G, N-terminal / Disulfide bond isomerase protein N-terminal domain / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G / Thioredoxin-like domain / Thioredoxin-like fold / Nuclear Transport Factor 2; Chain: A, / Glutaredoxin / Glutaredoxin ...Disulphide bond isomerase, DsbC/G, N-terminal / Disulfide bond isomerase protein N-terminal domain / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G / Thioredoxin-like domain / Thioredoxin-like fold / Nuclear Transport Factor 2; Chain: A, / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbC
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, M. / Monzingo, A.F. / Segatori, L. / Georgiou, G. / Robertus, J.D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of DsbC from Haemophilus influenzae.
Authors: Zhang, M. / Monzingo, A.F. / Segatori, L. / Georgiou, G. / Robertus, J.D.
History
DepositionApr 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein dsbC


Theoretical massNumber of molelcules
Total (without water)23,5321
Polymers23,5321
Non-polymers00
Water18010
1
A: Thiol:disulfide interchange protein dsbC

A: Thiol:disulfide interchange protein dsbC


Theoretical massNumber of molelcules
Total (without water)47,0642
Polymers47,0642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+3/21
Unit cell
Length a, b, c (Å)74.920, 74.920, 103.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe second part of the biological dimer is generated by the two-fold axis: -y, -x, 3/2-z

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Components

#1: Protein Thiol:disulfide interchange protein dsbC


Mass: 23532.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: DSBC, XPRA, HI1213 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: P45111, protein disulfide-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.1 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, sodium phosphate, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 19, 2002
RadiationMonochromator: DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→40 Å / Num. all: 7826 / Num. obs: 7826 / % possible obs: 71.3 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 20.1
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 3.4 / % possible all: 35.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EEJ

1eej


Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: DUE TO THE EXTREME ANISOTROPY OF THE DATA, A THREE DIMENSIONAL ELLIPSOID WITH RESOLUTION LIMITS CORRESPONDING TO THE MAXIMUM DIFFRACTION IN EACH DIRECTION WAS DEFINED TO SELECT REFLECTIONS ...Details: DUE TO THE EXTREME ANISOTROPY OF THE DATA, A THREE DIMENSIONAL ELLIPSOID WITH RESOLUTION LIMITS CORRESPONDING TO THE MAXIMUM DIFFRACTION IN EACH DIRECTION WAS DEFINED TO SELECT REFLECTIONS USED IN REFINEMENT. THESE DIFFRACTION LIMITS WERE 2.5, 3.3, 3.3. ANGSTROMS. THE 2.5 A DIRECTION CORRESPONDS TO THE C* AXIS, THE 3.3 A DIRECTIONS CORRESPONDS TO THE A* AND B* AXES.
RfactorNum. reflectionSelection details
Rfree0.295 374 RANDOM
Rwork0.246 --
obs0.249 6999 -
all-7369 -
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 0 10 1574
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.407

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