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- PDB-2h1b: ResA E80Q -

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Basic information

Entry
Database: PDB / ID: 2h1b
TitleResA E80Q
ComponentsThiol-disulfide oxidoreductase resA
KeywordsOXIDOREDUCTASE / ResA / ResA E80Q / E80Q / Thioredoxin
Function / homology
Function and homology information


cytochrome complex assembly / disulfide oxidoreductase activity / antioxidant activity / plasma membrane
Similarity search - Function
Thiol-disulphide oxidoreductase ResA / : / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Thiol-disulphide oxidoreductase ResA / : / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Thiol-disulfide oxidoreductase ResA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLewin, A. / Crow, A. / Oubrie, A. / Le Brun, N.E.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Molecular Basis for Specificity of the Extracytoplasmic Thioredoxin ResA.
Authors: Lewin, A. / Crow, A. / Oubrie, A. / Le Brun, N.E.
History
DepositionMay 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Aug 30, 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: Thiol-disulfide oxidoreductase resA
B: Thiol-disulfide oxidoreductase resA
C: Thiol-disulfide oxidoreductase resA
D: Thiol-disulfide oxidoreductase resA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,25812
Polymers63,7654
Non-polymers4948
Water10,395577
1
A: Thiol-disulfide oxidoreductase resA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1865
Polymers15,9411
Non-polymers2454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol-disulfide oxidoreductase resA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0653
Polymers15,9411
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thiol-disulfide oxidoreductase resA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0032
Polymers15,9411
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Thiol-disulfide oxidoreductase resA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0032
Polymers15,9411
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.969, 46.511, 95.054
Angle α, β, γ (deg.)90.00, 105.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thiol-disulfide oxidoreductase resA


Mass: 15941.146 Da / Num. of mol.: 4 / Mutation: E80Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: resA / Production host: Escherichia coli (E. coli) / References: UniProt: P35160
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 27 - 30 % PEG 4,000, 0.1 M Sodium Citrate pH 5 - 5.8, 0.2 M Ammonium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 7, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.95→91.67 Å / Num. all: 39655 / Num. obs: 39655 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 9.3
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 4.5 / Num. measured all: 21977 / Num. unique all: 5730 / Rsym value: 0.148 / % possible all: 100

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.8 Å29.46 Å
Translation2.8 Å29.46 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ProDCdata collection
MOSFLMdata reduction
CCP4(SCALA)data reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SU9

1su9


Resolution: 1.95→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.056 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1993 5 %RANDOM
Rwork0.151 ---
all0.153 39655 --
obs0.176 39643 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.041 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.1 Å2
2--0.22 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4473 0 32 577 5082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224629
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9576289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0465591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0525.268205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15115809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0281512
X-RAY DIFFRACTIONr_chiral_restr0.1060.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023514
X-RAY DIFFRACTIONr_nbd_refined0.2080.22299
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23102
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2461
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.2115
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.275
X-RAY DIFFRACTIONr_mcbond_it0.7861.52916
X-RAY DIFFRACTIONr_mcangle_it1.29624621
X-RAY DIFFRACTIONr_scbond_it1.95331970
X-RAY DIFFRACTIONr_scangle_it2.9884.51651
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 144 -
Rwork0.16 2778 -
obs-2922 99.97 %

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