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- PDB-2h1g: ResA C74A/C77A -

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Basic information

Entry
Database: PDB / ID: 2h1g
TitleResA C74A/C77A
ComponentsThiol-disulfide oxidoreductase resA
KeywordsOXIDOREDUCTASE / ResA / double mutant / C77A / C74A / ResA C74A/C77A / 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: 3.1 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / 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


Theoretical massNumber of molelcules
Total (without water)31,7562
Polymers31,7562
Non-polymers00
Water23413
1
A: Thiol-disulfide oxidoreductase resA


Theoretical massNumber of molelcules
Total (without water)15,8781
Polymers15,8781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol-disulfide oxidoreductase resA


Theoretical massNumber of molelcules
Total (without water)15,8781
Polymers15,8781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.031, 59.522, 109.562
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
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
12B
22A
32B
42A
52B
62A
72B
82A
92B
102A
112B
122A
132B
142A
152B
162A
172B
182A
192B
202A

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERLYSLYS1AA40 - 534 - 17
211SERSERLYSLYS1BB40 - 534 - 17
321ARGARGARGARG3AA5418
421ARGARGARGARG3BB5418
531ILEILELYSLYS1AA55 - 7819 - 42
631ILEILELYSLYS1BB55 - 7819 - 42
741LYSLYSLYSLYS3AA7943
841LYSLYSLYSLYS3BB7943
951GLUGLULYSLYS1AA80 - 8944 - 53
1051GLUGLULYSLYS1BB80 - 8944 - 53
1161HISHISHISHIS3AA9054
1261HISHISHISHIS3BB9054
1371PHEPHEVALVAL1AA91 - 11055 - 74
1471PHEPHEVALVAL1BB91 - 11055 - 74
1581HISHISHISHIS5AA11175
1681HISHISHISHIS5BB11175
1791ASNASNVALVAL1AA112 - 13776 - 101
1891ASNASNVALVAL1BB112 - 13776 - 101
19101PROPROPROPRO1AA141 - 174105 - 138
20101PROPROPROPRO1BB141 - 174105 - 138
112SERSERLYSLYS1BB40 - 534 - 17
212SERSERLYSLYS1AA40 - 534 - 17
322ARGARGARGARG3BB5418
422ARGARGARGARG3AA5418
532ILEILELYSLYS1BB55 - 7819 - 42
632ILEILELYSLYS1AA55 - 7819 - 42
742LYSLYSLYSLYS3BB7943
842LYSLYSLYSLYS3AA7943
952GLUGLULYSLYS1BB80 - 8944 - 53
1052GLUGLULYSLYS1AA80 - 8944 - 53
1162HISHISHISHIS3BB9054
1262HISHISHISHIS3AA9054
1372PHEPHEVALVAL1BB91 - 11055 - 74
1472PHEPHEVALVAL1AA91 - 11055 - 74
1582HISHISHISHIS5BB11175
1682HISHISHISHIS5AA11175
1792ASNASNVALVAL1BB112 - 13776 - 101
1892ASNASNVALVAL1AA112 - 13776 - 101
19102PROPROPROPRO1BB141 - 174105 - 138
20102PROPROPROPRO1AA141 - 174105 - 138

NCS ensembles :
ID
1
2

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Components

#1: Protein Thiol-disulfide oxidoreductase resA


Mass: 15878.000 Da / Num. of mol.: 2 / Mutation: C77A, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20 % - 27 % PEG 4,000, 0.1 M MES pH 5.6, 0.1 M Ammonium Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0688 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: 1.0688 Å / Relative weight: 1
ReflectionResolution: 3.1→55.048 Å / Num. all: 5722 / Num. obs: 5722 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 4.6
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.2 / Num. measured all: 4118 / Num. unique all: 761 / Rsym value: 0.296 / % possible all: 91.9

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.2 Å36.9 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: 3.1→37.16 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.848 / SU B: 21.411 / SU ML: 0.383 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.534 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 298 5.2 %Free set copied from 1SU9 and extended as necessary.
Rwork0.185 ---
all0.189 5695 --
obs0.238 5695 95.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 3.1→37.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 0 13 2166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222207
X-RAY DIFFRACTIONr_angle_refined_deg2.0441.9532994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9525271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03325.46497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.83215376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.763154
X-RAY DIFFRACTIONr_chiral_restr0.1270.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021664
X-RAY DIFFRACTIONr_nbd_refined0.240.21002
X-RAY DIFFRACTIONr_nbtor_refined0.3330.21505
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.262
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0760.23
X-RAY DIFFRACTIONr_mcbond_it0.8561.51387
X-RAY DIFFRACTIONr_mcangle_it1.50322212
X-RAY DIFFRACTIONr_scbond_it2.2533926
X-RAY DIFFRACTIONr_scangle_it3.9134.5782
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1019TIGHT POSITIONAL0.090.05
1A4MEDIUM POSITIONAL0.10.5
1A24LOOSE POSITIONAL1.465
1A1019TIGHT THERMAL0.110.5
1A4MEDIUM THERMAL0.232
1A24LOOSE THERMAL6.8310
2B1019TIGHT POSITIONAL0.090.05
2B4MEDIUM POSITIONAL0.10.5
2B24LOOSE POSITIONAL1.465
2B1019TIGHT THERMAL0.110.5
2B4MEDIUM THERMAL0.232
2B24LOOSE THERMAL6.8310
LS refinement shellResolution: 3.102→3.182 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 18 -
Rwork0.242 364 -
obs-382 89.25 %

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