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- PDB-4pwo: Crystal structure of DsbA from the Gram positive bacterium Coryne... -

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Basic information

Entry
Database: PDB / ID: 4pwo
TitleCrystal structure of DsbA from the Gram positive bacterium Corynebacterium diphtheriae
ComponentsDsbA
KeywordsSTRUCTURAL GENOMICS / thioredoxin domain / disulfided bond isomerase
Function / homology: / DsbA, N-terminal domain / Thioredoxin / Thioredoxin-like fold / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / membrane / Secreted protein
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsUm, S.H. / Kim, J.S. / Jiao, L. / Yoon, B.Y. / Jo, I. / Ha, N.C.
CitationJournal: To be Published
Title: Crystal structure and biochemical characterization of DsbA from the Gram positive bacterium Corynebacterium diphtheriae
Authors: Um, S.H. / Kim, J.S. / Jiao, L. / Yoon, B.Y. / Jo, I. / Ha, N.C.
History
DepositionMar 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9532
Polymers26,8611
Non-polymers921
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.638, 68.318, 69.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DsbA


Mass: 26860.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NJK4*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 287 K / pH: 8.5
Details: 0.2M sodium acetate, 0.1M Tris-HCl pH 8.5, 30% PEG4K, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2013
RadiationMonochromator: DOUBLE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 36061 / % possible obs: 99.8 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.52→1.55 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
Cootmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PWP

4pwp


Resolution: 1.52→19.93 Å / SU ML: 0.13 / σ(F): 1.54 / Phase error: 17.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 1801 4.99 %
Rwork0.167 --
obs0.168 34302 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 6 195 2094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062047
X-RAY DIFFRACTIONf_angle_d1.0682799
X-RAY DIFFRACTIONf_dihedral_angle_d13.515783
X-RAY DIFFRACTIONf_chiral_restr0.072304
X-RAY DIFFRACTIONf_plane_restr0.005378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5197-1.56080.22761250.17732590X-RAY DIFFRACTION99
1.5608-1.60670.21431360.1712593X-RAY DIFFRACTION100
1.6067-1.65860.25581380.17312604X-RAY DIFFRACTION100
1.6586-1.71780.21171410.16792593X-RAY DIFFRACTION100
1.7178-1.78650.19491260.16482638X-RAY DIFFRACTION100
1.7865-1.86780.2171300.16542624X-RAY DIFFRACTION100
1.8678-1.96620.22751540.17112602X-RAY DIFFRACTION100
1.9662-2.08920.19921350.16932637X-RAY DIFFRACTION100
2.0892-2.25040.18771390.15952627X-RAY DIFFRACTION100
2.2504-2.47640.19631530.17082646X-RAY DIFFRACTION100
2.4764-2.83390.21871380.18072666X-RAY DIFFRACTION100
2.8339-3.56710.18831370.17282695X-RAY DIFFRACTION100
3.5671-19.93480.15851490.15372783X-RAY DIFFRACTION99

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