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- PDB-4fyb: Structural and functional characterizations of a thioredoxin-fold... -

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Basic information

Entry
Database: PDB / ID: 4fyb
TitleStructural and functional characterizations of a thioredoxin-fold protein from Helicobacter pylori
ComponentsThiol:disulfide interchange protein (DsbC)
KeywordsOXIDOREDUCTASE / Thioredoxin fold / Reductase
Function / homologySoxW family / Thioredoxin-like domain / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Thiol:disulfide interchange protein (DsbC), putative
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsYoon, J.Y. / Kim, J. / Lee, S.J. / Im, H.N. / Kim, H.S. / Yoon, H. / An, D.R. / Kim, J.Y. / Kim, S. / Han, B.W. / Suh, S.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural and functional characterization of HP0377, a thioredoxin-fold protein from Helicobacter pylori
Authors: Yoon, J.Y. / Kim, J. / An, D.R. / Lee, S.J. / Kim, H.S. / Im, H.N. / Yoon, H.J. / Kim, J.Y. / Kim, S.J. / Han, B.W. / Suh, S.W.
History
DepositionJul 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
B: Thiol:disulfide interchange protein (DsbC)
A: Thiol:disulfide interchange protein (DsbC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1883
Polymers55,0962
Non-polymers921
Water2,360131
1
B: Thiol:disulfide interchange protein (DsbC)


Theoretical massNumber of molelcules
Total (without water)27,5481
Polymers27,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Thiol:disulfide interchange protein (DsbC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6402
Polymers27,5481
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.575, 43.913, 80.059
Angle α, β, γ (deg.)90.00, 108.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thiol:disulfide interchange protein (DsbC)


Mass: 27548.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: HP_0377 / Production host: Escherichia coli (E. coli) / References: UniProt: O25140
#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.: 131 / 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: 2.02 Å3/Da / Density % sol: 39.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 200mM potassium acetate (pH 7.8), 20% (w/v) polyethylene glycol (PEG) 1500, 2.2mM FOS-Choline-8 (fluorinated), VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.2398 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 22650 / Num. obs: 22514 / % possible obs: 99.4 %
Reflection shellResolution: 2.2→2.28 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AutoSolphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.267 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23026 1154 5.1 %RANDOM
Rwork0.19539 ---
obs0.19727 21360 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.383 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å20 Å2-1.3 Å2
2--0.34 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 6 131 2772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022706
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.983633
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8985325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5625.556126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54915531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.385156
X-RAY DIFFRACTIONr_chiral_restr0.0790.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021996
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 74 -
Rwork0.24 1348 -
obs--91.98 %

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