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- PDB-2h1a: ResA C74A Variant -

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Basic information

Entry
Database: PDB / ID: 2h1a
TitleResA C74A Variant
ComponentsThiol-disulfide oxidoreductase resA
KeywordsOXIDOREDUCTASE / ResA / C74A / Mutant / 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
Thiol-disulfide oxidoreductase ResA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.5Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9444
Polymers31,8202
Non-polymers1242
Water2,432135
1
A: Thiol-disulfide oxidoreductase resA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0343
Polymers15,9101
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol-disulfide oxidoreductase resA


Theoretical massNumber of molelcules
Total (without water)15,9101
Polymers15,9101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.874, 59.596, 109.771
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13B
23A
14B
24A

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERASPASPAA40 - 1364 - 100
21SERSERASPASPBB40 - 1364 - 100
12PROPROLYSLYSAA141 - 173105 - 137
22PROPROLYSLYSBB141 - 173105 - 137
13SERSERASPASPBB40 - 1364 - 100
23SERSERASPASPAA40 - 1364 - 100
14PROPROLYSLYSBB141 - 173105 - 137
24PROPROLYSLYSAA141 - 173105 - 137

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Thiol-disulfide oxidoreductase resA


Mass: 15910.064 Da / Num. of mol.: 2 / Mutation: C74A
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 25 - 30 % PEG 4,000, 0.1 M Sodium Citrate pH 5.4 - 5.8, 0.2M Ammonium Acetate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 12619 / Num. obs: 12619 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rsym value: 0.136 / Net I/σ(I): 13.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 5.4 / Rsym value: 0.35 / % possible all: 100

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.8 Å43.11 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 / Resolution: 2.4→40 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.885 / SU B: 7.781 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.417 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 642 5.1 %Copied from 1SU9 free set and extended as necessary
Rwork0.177 ---
all0.18 12619 --
obs0.207 12578 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.318 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å20 Å2
2--1.36 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 8 135 2354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222278
X-RAY DIFFRACTIONr_angle_refined_deg1.931.9553092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6315284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24125.25399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.60915393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.429155
X-RAY DIFFRACTIONr_chiral_restr0.1450.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021719
X-RAY DIFFRACTIONr_nbd_refined0.210.2964
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21503
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.2105
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.210
X-RAY DIFFRACTIONr_mcbond_it0.9251.51433
X-RAY DIFFRACTIONr_mcangle_it1.65422282
X-RAY DIFFRACTIONr_scbond_it2.6153962
X-RAY DIFFRACTIONr_scangle_it4.1334.5807
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A381TIGHT POSITIONAL0.080.05
1A366LOOSE POSITIONAL0.45
1A381TIGHT THERMAL0.160.5
1A366LOOSE THERMAL2.210
2A132TIGHT POSITIONAL0.050.05
2A125LOOSE POSITIONAL0.345
2A132TIGHT THERMAL0.150.5
2A125LOOSE THERMAL1.7810
3B381TIGHT POSITIONAL0.080.05
3B366LOOSE POSITIONAL0.45
3B381TIGHT THERMAL0.160.5
3B366LOOSE THERMAL2.210
4B132TIGHT POSITIONAL0.050.05
4B125LOOSE POSITIONAL0.345
4B132TIGHT THERMAL0.150.5
4B125LOOSE THERMAL1.7810
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 47 -
Rwork0.209 879 -
obs-926 99.89 %

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