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- PDB-3hxs: Crystal Structure of Bacteroides fragilis TrxP -

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Basic information

Entry
Database: PDB / ID: 3hxs
TitleCrystal Structure of Bacteroides fragilis TrxP
ComponentsThioredoxin
KeywordsELECTRON TRANSPORT / thioredoxin
Function / homology
Function and homology information


protein-disulfide reductase activity / metal ion binding / cytoplasm
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: 1.996 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, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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: Thioredoxin
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1204
Polymers31,9892
Non-polymers1312
Water3,783210
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-61 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.568, 94.568, 82.518
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: 15994.347 Da / Num. of mol.: 2 / Fragment: residues in UNP 43-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: 638R / Gene: trxP / Plasmid: pMALp2X / 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


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 16%(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: 0.99901 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jul 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99901 Å / Relative weight: 1
ReflectionResolution: 1.996→66.87 Å / Num. all: 25931 / Num. obs: 25931 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.9 % / Biso Wilson estimate: 34.003 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 8.055
Reflection shellResolution: 2→2.1 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 1.2 / Num. measured all: 50695 / Num. unique all: 3597 / Rsym value: 0.645 / % possible all: 96.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.71 Å
Translation2.5 Å19.71 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.17data scaling
PHASER1.3.3phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2TRX

2trx


Resolution: 1.996→19.713 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.836 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1249 4.83 %random
Rwork0.196 24629 --
all0.198 25931 --
obs0.198 25878 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.234 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 111.32 Å2 / Biso mean: 41.279 Å2 / Biso min: 14.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å2-0 Å2
2--2.23 Å20 Å2
3----4.46 Å2
Refinement stepCycle: LAST / Resolution: 1.996→19.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 2 210 2147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061992
X-RAY DIFFRACTIONf_angle_d1.0372694
X-RAY DIFFRACTIONf_chiral_restr0.074285
X-RAY DIFFRACTIONf_plane_restr0.004339
X-RAY DIFFRACTIONf_dihedral_angle_d17.776742
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.996-2.0760.2851090.2472591270096
2.076-2.170.2921270.2327152842100
2.17-2.2840.2571410.21427012842100
2.284-2.4270.2741300.20827272857100
2.427-2.6140.271550.20327082863100
2.614-2.8760.271470.21827212868100
2.876-3.2910.2951430.20927532896100
3.291-4.140.2131480.16727902938100
4.14-19.7140.1771490.16629233072100

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