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- PDB-3zij: Crystal structure of the thioredoxin-like protein BC3987 -

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Basic information

Entry
Database: PDB / ID: 3zij
TitleCrystal structure of the thioredoxin-like protein BC3987
ComponentsTHIOREDOXIN
KeywordsOXIDOREDUCTASE / GLUTAREDOXIN / DISULFIDE / 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: 1.4 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 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Dec 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 1.3Nov 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)18,0112
Polymers18,0112
Non-polymers00
Water1,78399
1
A: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)9,0051
Polymers9,0051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)9,0051
Polymers9,0051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.700, 98.870, 25.070
Angle α, β, γ (deg.)90.00, 91.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein THIOREDOXIN


Mass: 9005.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS CEREUS (bacteria) / 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.: 99 / 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: 1.4 Å3/Da / Density % sol: 29 % / 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: 0.975948
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975948 Å / Relative weight: 1
ReflectionResolution: 1.4→33 Å / Num. obs: 22238 / % possible obs: 94.3 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 15
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 6.1 / % possible all: 93.8

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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 1R7H

1r7h


Resolution: 1.4→32.98 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.318 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20537 1146 5.2 %RANDOM
Rwork0.18787 ---
obs0.18881 21061 94.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.879 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20 Å20.75 Å2
2---0.75 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.4→32.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 0 99 1304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.021254
X-RAY DIFFRACTIONr_bond_other_d0.0010.021206
X-RAY DIFFRACTIONr_angle_refined_deg2.4351.9731707
X-RAY DIFFRACTIONr_angle_other_deg1.1143.0032783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.245153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.07825.62564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60915223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.113155
X-RAY DIFFRACTIONr_chiral_restr0.1480.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211413
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02272
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 86 -
Rwork0.256 1567 -
obs--93.76 %

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