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- PDB-3gh9: Crystal structure of EDTA-treated BdbD (Oxidised) -

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Basic information

Entry
Database: PDB / ID: 3gh9
TitleCrystal structure of EDTA-treated BdbD (Oxidised)
ComponentsDisulfide bond formation protein D
KeywordsOXIDOREDUCTASE / BdbD / DsbA / Trx-like / Competence / Disulfide bond / Redox-active center
Function / homology
Function and homology information


establishment of competence for transformation / oxidoreductase activity / membrane raft / plasma membrane
Similarity search - Function
Thioredoxin / Thioredoxin-like fold / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Disulfide bond formation protein D
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsCrow, A. / Lewin, A. / Hederstedt, L. / Le-Brun, N.E.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal Structure and Biophysical Properties of Bacillus subtilis BdbD: AN OXIDIZING THIOL:DISULFIDE OXIDOREDUCTASE CONTAINING A NOVEL METAL SITE
Authors: Crow, A. / Lewin, A. / Hecht, O. / Carlsson Moller, M. / Moore, G.R. / Hederstedt, L. / Le Brun, N.E.
History
DepositionMar 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_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 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disulfide bond formation protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1063
Polymers23,0441
Non-polymers622
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.550, 43.570, 54.560
Angle α, β, γ (deg.)90.00, 107.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Disulfide bond formation protein D / Disulfide oxidoreductase D / Thiol-disulfide oxidoreductase D


Mass: 23043.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 1A1 / Gene: bdbD, BSU33480, yvgV / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: O32218
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.9 Å3/Da / Density % sol: 35.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25-27 % PEG2000, 100mM Ammonium Acetate, 100mM MES, pH6.5, 100uM EDTA, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9798 Å
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.69→36.79 Å / Num. all: 18095 / Num. obs: 18095 / % possible obs: 92.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rsym value: 0.052 / Net I/σ(I): 19.9
Reflection shellResolution: 1.69→1.78 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.286 / % possible all: 66.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BP3model building
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
BP3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EU3

3eu3


Resolution: 1.69→36.79 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.992 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.407 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25004 914 5.1 %RANDOM
Rwork0.19503 ---
obs0.19784 17169 92.58 %-
all-18095 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.136 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å2-0.16 Å2
2--1.07 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.69→36.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 5 142 1767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221673
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9672276
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9565218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16927.01377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29215325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.672151
X-RAY DIFFRACTIONr_chiral_restr0.0810.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211290
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8221.51024
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39321687
X-RAY DIFFRACTIONr_scbond_it2.0273649
X-RAY DIFFRACTIONr_scangle_it3.1844.5587
X-RAY DIFFRACTIONr_rigid_bond_restr1.19431673
X-RAY DIFFRACTIONr_sphericity_free4.2763143
X-RAY DIFFRACTIONr_sphericity_bonded3.31931624
LS refinement shellResolution: 1.69→1.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 39 -
Rwork0.288 831 -
obs--61.05 %

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