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- PDB-3zit: Crystal structure of the thioredoxin-like protein BC3987 mutant T8A -

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Basic information

Entry
Database: PDB / ID: 3zit
TitleCrystal structure of the thioredoxin-like protein BC3987 mutant T8A
ComponentsTHIOREDOXIN
KeywordsOXIDOREDUCTASE / GLUTAREDOXIN / TRX / GRX
Function / homology
Function and homology information


cell redox homeostasis / electron transfer activity
Similarity search - Function
Glutaredoxin-like protein, YruB / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBACILLUS CEREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsRohr, A.K. / Hammerstad, M. / Andersson, K.K.
CitationJournal: Plos One / Year: 2013
Title: Tuning of Thioredoxin Redox Properties by Intramolecular Hydrogen Bonds.
Authors: Rohr, A.K. / Hammerstad, M. / Andersson, K.K.
History
DepositionJan 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Structure summary
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOREDOXIN
B: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)17,9502
Polymers17,9502
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-8.6 kcal/mol
Surface area8660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.410, 99.090, 25.160
Angle α, β, γ (deg.)90.00, 91.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein THIOREDOXIN


Mass: 8975.234 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q819J1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 1.72 Å3/Da / Density % sol: 28 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES PH 7.5, 50 MM MGCL2 AND 30 % (W/V) POLYETHYLENE GLYCOL MONOMETHYL ETHER 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976273
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976273 Å / Relative weight: 1
ReflectionResolution: 1.18→24.78 Å / Num. obs: 31318 / % possible obs: 84.9 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.1
Reflection shellResolution: 1.18→1.25 Å / Redundancy: 3 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.9 / % possible all: 83.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZIJ

3zij


Resolution: 1.18→24.78 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.198 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 1655 5 %RANDOM
Rwork0.14354 ---
obs0.14624 31318 84.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.814 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å2-0.4 Å2
2--0.19 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.18→24.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 0 0 89 1315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.021290
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3991.9721757
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1635159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02625.88268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21615229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.872155
X-RAY DIFFRACTIONr_chiral_restr0.1390.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021991
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr15.91631290
X-RAY DIFFRACTIONr_sphericity_free30.816521
X-RAY DIFFRACTIONr_sphericity_bonded16.66451328
LS refinement shellResolution: 1.182→1.213 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 128 -
Rwork0.173 2273 -
obs--84.01 %

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