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

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Basic information

Entry
Database: PDB / ID: 4fyc
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 / MOLECULAR REPLACEMENT / Resolution: 2.31 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 1.2Nov 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_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
A: Thiol:disulfide interchange protein (DsbC)
B: Thiol:disulfide interchange protein (DsbC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2913
Polymers55,0962
Non-polymers1941
Water1,13563
1
A: Thiol:disulfide interchange protein (DsbC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7422
Polymers27,5481
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
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
Unit cell
Length a, b, c (Å)140.858, 43.953, 76.699
Angle α, β, γ (deg.)90.00, 112.29, 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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 1.99 Å3/Da / Density % sol: 38.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200mM sodium formate (pH 7.0), 20% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 19138 / Num. obs: 17837 / % possible obs: 93.2 %

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FYB

4fyb


Resolution: 2.31→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.685 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23804 910 5.1 %RANDOM
Rwork0.19061 ---
obs0.19303 16927 92.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.933 Å2
Baniso -1Baniso -2Baniso -3
1--4.19 Å20 Å2-2.37 Å2
2---1.92 Å20 Å2
3---4.31 Å2
Refinement stepCycle: LAST / Resolution: 2.31→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2633 0 13 63 2709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022702
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9843616
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.635321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.73925.556126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71915528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.015156
X-RAY DIFFRACTIONr_chiral_restr0.0810.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021980
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: 2.314→2.374 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 40 -
Rwork0.255 977 -
obs--76.29 %

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