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- PDB-3eu3: Crystal Structure of BdbD from Bacillus subtilis (reduced) -

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Basic information

Entry
Database: PDB / ID: 3eu3
TitleCrystal Structure of BdbD from Bacillus subtilis (reduced)
ComponentsBdbD
KeywordsOXIDOREDUCTASE / bdbd / Dsba-like / thioredoxin-like / dithiol form / Competence / 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 / Resolution: 1.5 Å
AuthorsCrow, A. / Moller, M.C. / 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
DepositionOct 9, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: BdbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1463
Polymers23,0441
Non-polymers1022
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.774, 43.399, 54.658
Angle α, β, γ (deg.)90.00, 107.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BdbD / Bacillus disulfide bond protein D


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 1.9 Å3/Da / Density % sol: 35.41 %
Crystal growpH: 6.5
Details: 27% PEG2000, 0.1M ammonium acetate, 0.1M MES, pH6.5, 1mM DTT,cryo-protected with 20% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→28.21 Å / Num. all: 27450 / Num. obs: 27450 / % possible obs: 97.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rsym value: 0.052 / Net I/σ(I): 15
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 27450 / Rsym value: 0.267 / % possible all: 89.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BP3model building
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
BP3phasing
RefinementResolution: 1.5→26.08 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.254 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, THE DEPOSITORS ASSERT THAT NO BACKBONE TORSION (RAMACHANDRAN PLOT) OUTLIERS ARE PRESENT AS JUDGED BY THE STANDARDS EMPLOYED BY MOLPROBITY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, THE DEPOSITORS ASSERT THAT NO BACKBONE TORSION (RAMACHANDRAN PLOT) OUTLIERS ARE PRESENT AS JUDGED BY THE STANDARDS EMPLOYED BY MOLPROBITY (V3.15), OR PROCHECK (V3.4.4).
RfactorNum. reflection% reflectionSelection details
Rfree0.21919 1385 5 %RANDOM
Rwork0.18608 ---
obs0.18776 26211 98.83 %-
all-26211 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.639 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å2-0.05 Å2
2--0.9 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 1.5→26.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 0 5 117 1660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221582
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9672148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2515203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32727.14377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00615298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1.856151
X-RAY DIFFRACTIONr_chiral_restr0.0820.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021207
X-RAY DIFFRACTIONr_nbd_refined0.2040.2796
X-RAY DIFFRACTIONr_nbtor_refined0.310.21122
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0910.294
X-RAY DIFFRACTIONr_metal_ion_refined0.090.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3120.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.211
X-RAY DIFFRACTIONr_mcbond_it1.0291.5984
X-RAY DIFFRACTIONr_mcangle_it1.60521580
X-RAY DIFFRACTIONr_scbond_it2.2113664
X-RAY DIFFRACTIONr_scangle_it3.2864.5562
X-RAY DIFFRACTIONr_rigid_bond_restr1.36131648
X-RAY DIFFRACTIONr_sphericity_free4.7293118
X-RAY DIFFRACTIONr_sphericity_bonded3.61231542
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 96 -
Rwork0.267 1735 -
obs--90.69 %

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