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- PDB-3hyp: Crystal structure of Bacteroides fragilis TrxP_S105G mutant -

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Basic information

Entry
Database: PDB / ID: 3hyp
TitleCrystal structure of Bacteroides fragilis TrxP_S105G mutant
ComponentsThioredoxin
KeywordsELECTRON TRANSPORT / thioredoxin / disulfide bond
Function / homology
Function and homology information


protein-disulfide reductase activity / metal ion binding
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Thioredoxin-like superfamily ...Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / 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
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.899 Å
AuthorsShouldice, S.R.
CitationJournal: Mol.Microbiol. / Year: 2010
Title: In vivo oxidative protein folding can be facilitated by oxidation-reduction cycling
Authors: Shouldice, S.R. / Cho, S.H. / Boyd, D. / Heras, B. / Eser, M. / Beckwith, J. / Riggs, P. / Martin, J.L. / Berkmen, M.
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0594
Polymers31,9292
Non-polymers1312
Water1,72996
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-62 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.506, 94.506, 82.539
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsTHE DEPOSITORS HAVE EVIDENCE (GEL FILTRATION) THAT SUPPORTS A DIMER AS THE BIOLOGICALLY ACTIVE MOLECULE, HOWEVER A MONOMER CAN NOT BE ENTIRELY EXCLUDED.

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Components

#1: Protein Thioredoxin / / TrxP


Mass: 15964.321 Da / Num. of mol.: 2 / Fragment: residues in UNP 21-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: 638R / Gene: trxP / Plasmid: pMAL-c4X / Production host: Escherichia coli (E. coli) / Strain (production host): NEB Express / References: UniProt: Q64SV7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.89 Å3/Da / Density % sol: 57.38 % / Mosaicity: 0.554 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 15%(w/v) PEG 6000, 0.01M ZnCl2, 0.1M MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95364 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
ReflectionResolution: 2.899→50 Å / Num. all: 8745 / Num. obs: 8745 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.7 % / Rmerge(I) obs: 0.117 / Χ2: 0.924 / Net I/σ(I): 30.583
Reflection shellResolution: 2.9→3 Å / Redundancy: 21.5 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 4.2 / Num. unique all: 839 / Χ2: 0.762 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.76
Highest resolutionLowest resolution
Rotation2.9 Å29.89 Å
Translation2.9 Å29.89 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.1phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3HXS

3hxs


Resolution: 2.899→29.885 Å / Occupancy max: 1 / Occupancy min: 0.7 / FOM work R set: 0.805 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.263 408 4.68 %random
Rwork0.197 ---
all0.2 8745 --
obs0.2 8712 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.662 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso max: 112.06 Å2 / Biso mean: 51.748 Å2 / Biso min: 26.72 Å2
Baniso -1Baniso -2Baniso -3
1--1.287 Å2-0 Å20 Å2
2---1.287 Å2-0 Å2
3---2.574 Å2
Refinement stepCycle: LAST / Resolution: 2.899→29.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 2 96 2005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071960
X-RAY DIFFRACTIONf_angle_d0.9282645
X-RAY DIFFRACTIONf_chiral_restr0.06278
X-RAY DIFFRACTIONf_plane_restr0.004333
X-RAY DIFFRACTIONf_dihedral_angle_d17.678727
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.899-30.3141390.2326912830
3.318-4.1780.2691320.17627382870
4.178-29.8870.2331370.18628753012

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