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- PDB-3c73: Structure of CEHC variant ResA -

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Basic information

Entry
Database: PDB / ID: 3c73
TitleStructure of CEHC variant ResA
ComponentsThiol-disulfide oxidoreductase resA
KeywordsOXIDOREDUCTASE / Thioredoxin-like fold / Cytochrome c-type biogenesis / Membrane / Redox-active center / Signal-anchor / Transmembrane
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: 2.5 Å
AuthorsCrow, A.
CitationJournal: Biochem.J. / Year: 2008
Title: Effects of substitutions in the CXXC active-site motif of the extracytoplasmic thioredoxin ResA.
Authors: Lewin, A. / Crow, A. / Hodson, C.T. / Hederstedt, L. / Le Brun, N.E.
History
DepositionFeb 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 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 1.4Feb 21, 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)31,5163
Polymers31,4202
Non-polymers961
Water1,09961
1
A: Thiol-disulfide oxidoreductase resA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8062
Polymers15,7101
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiol-disulfide oxidoreductase resA


Theoretical massNumber of molelcules
Total (without water)15,7101
Polymers15,7101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.219, 60.169, 110.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
12B
22A
32B
42A
52B
62A
72B
82A
92B
102A

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERGLYGLYAA40 - 521 - 13
211SERSERGLYGLYBB40 - 521 - 13
321ARGARGASPASPAA54 - 5915 - 20
421ARGARGASPASPBB54 - 5915 - 20
531LYSLYSTHRTHRAA61 - 7222 - 33
631LYSLYSTHRTHRBB61 - 7222 - 33
741CYSCYSALAALAAA77 - 10938 - 70
841CYSCYSALAALABB77 - 10938 - 70
951HISHISGLYGLYAA111 - 17572 - 136
1051HISHISGLYGLYBB111 - 17572 - 136
112SERSERGLYGLYBB40 - 521 - 13
212SERSERGLYGLYAA40 - 521 - 13
322ARGARGASPASPBB54 - 5915 - 20
422ARGARGASPASPAA54 - 5915 - 20
532LYSLYSTHRTHRBB61 - 7222 - 33
632LYSLYSTHRTHRAA61 - 7222 - 33
742CYSCYSALAALABB77 - 10938 - 70
842CYSCYSALAALAAA77 - 10938 - 70
952HISHISGLYGLYBB111 - 17572 - 136
1052HISHISGLYGLYAA111 - 17572 - 136

NCS ensembles :
ID
1
2

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Components

#1: Protein Thiol-disulfide oxidoreductase resA


Mass: 15709.917 Da / Num. of mol.: 2 / Fragment: UNP residues 40-179 / Mutation: P76H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: resA, ypxA / Production host: Escherichia coli (E. coli) / References: UniProt: P35160
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 27% PEG 4000, 0.1 M tri-Sodium Citrate pH 5.6, 0.2M Ammonium acetate, 10 mM DTT. Protein concentration 12mg/ml in 20 mM MOPS pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0688 Å
DetectorType: ADSC / Detector: CCD / Date: Feb 14, 2006
RadiationMonochromator: ESRF ID 23-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0688 Å / Relative weight: 1
ReflectionResolution: 2.5→52.85 Å / Num. all: 11418 / Num. obs: 11418 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Rsym value: 0.104 / Net I/σ(I): 14
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 6.5 / Num. unique all: 1636 / Rsym value: 0.276 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→35.88 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.88 / SU B: 8.586 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.534 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25298 582 5.1 %COPIED AND EXTENDED FROM 1SU9
Rwork0.17843 ---
obs0.18231 10799 99.78 %-
all-11418 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.008 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2--1.18 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 5 61 2286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222286
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.9443105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6435283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91525.096104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94115395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.78155
X-RAY DIFFRACTIONr_chiral_restr0.1140.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021731
X-RAY DIFFRACTIONr_nbd_refined0.2160.2929
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21496
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.25
X-RAY DIFFRACTIONr_mcbond_it1.0041.51438
X-RAY DIFFRACTIONr_mcangle_it1.71322267
X-RAY DIFFRACTIONr_scbond_it2.653988
X-RAY DIFFRACTIONr_scangle_it4.1554.5835
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A516medium positional0.240.5
2B516medium positional0.240.5
1A500loose positional0.475
2B500loose positional0.475
1A516medium thermal1.232
2B516medium thermal1.232
1A500loose thermal2.5210
2B500loose thermal2.5210
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 46 -
Rwork0.187 762 -
obs--100 %

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