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- PDB-2h1d: ResA pH 9.25 -

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Basic information

Entry
Database: PDB / ID: 2h1d
TitleResA pH 9.25
ComponentsThiol-disulfide oxidoreductase resA
KeywordsOXIDOREDUCTASE / ResA / High pH / 9.25 / pH 9.25 / ResA hiph
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: 2.6 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 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)31,9463
Polymers31,8842
Non-polymers621
Water81145
1
A: Thiol-disulfide oxidoreductase resA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0042
Polymers15,9421
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol-disulfide oxidoreductase resA


Theoretical massNumber of molelcules
Total (without water)15,9421
Polymers15,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.289, 59.791, 110.100
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
12B
22A
32B
42A

NCS domain segments:

Refine code: 3

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERVALVALAA40 - 1374 - 101
211SERSERVALVALBB40 - 1374 - 101
321PROPROGLYGLYAA141 - 175105 - 139
421PROPROGLYGLYBB141 - 175105 - 139
112SERSERVALVALBB40 - 1374 - 101
212SERSERVALVALAA40 - 1374 - 101
322PROPROGLYGLYBB141 - 175105 - 139
422PROPROGLYGLYAA141 - 175105 - 139

NCS ensembles :
ID
1
2
DetailsThe Biological Unit consists of a single ResA chain.

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Components

#1: Protein Thiol-disulfide oxidoreductase resA


Mass: 15942.131 Da / Num. of mol.: 2
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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.25
Details: Crystallized at pH 6.5 (30% PEG 4,000, 0.1 M MES, 0.2 M Ammonium Acetate) but then crystal soaked in a cryoprotectant at pH9.25 (MES component replaced by CHES pH 9.25) prior to data ...Details: Crystallized at pH 6.5 (30% PEG 4,000, 0.1 M MES, 0.2 M Ammonium Acetate) but then crystal soaked in a cryoprotectant at pH9.25 (MES component replaced by CHES pH 9.25) prior to data collection. The structure therefore represents a 'high pH soak'. See publication for further details., 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: 2.4→40 Å / Num. all: 9636 / Num. obs: 9636 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 6.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.6 / Num. measured all: 4975 / Num. unique all: 1409 / Rsym value: 0.247 / % possible all: 98.6

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.9 Å37.09 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: 2.6→37.16 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.842 / SU B: 10.843 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.412 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 496 5.2 %Copied free set from 1SU9 and extended with random reflections as required
Rwork0.195 ---
all0.2 9625 --
obs0.231 9625 95.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.412 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→37.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2157 0 4 45 2206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222214
X-RAY DIFFRACTIONr_angle_refined_deg1.8291.9553000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg75271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39425.46497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.92315380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.451154
X-RAY DIFFRACTIONr_chiral_restr0.1090.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021664
X-RAY DIFFRACTIONr_nbd_refined0.2220.2997
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21487
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.280
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.24
X-RAY DIFFRACTIONr_mcbond_it0.8681.51395
X-RAY DIFFRACTIONr_mcangle_it1.53622216
X-RAY DIFFRACTIONr_scbond_it2.7543941
X-RAY DIFFRACTIONr_scangle_it4.2914.5784
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A532TIGHT POSITIONAL0.080.05
1A521LOOSE POSITIONAL0.45
1A532TIGHT THERMAL0.150.5
1A521LOOSE THERMAL2.0410
2B532TIGHT POSITIONAL0.080.05
2B521LOOSE POSITIONAL0.45
2B532TIGHT THERMAL0.150.5
2B521LOOSE THERMAL2.0410
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 33 -
Rwork0.228 670 -
obs-703 97.5 %

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