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- PDB-3dvw: Crystal structure of reduced DsbA1 from Neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 3dvw
TitleCrystal structure of reduced DsbA1 from Neisseria meningitidis
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / thiol-oxidoreductase / neisseria / DsbA / disulfide bond
Function / homology
Function and homology information


disulfide oxidoreductase activity / periplasmic space
Similarity search - Function
Thioredoxin / Thiol:disulphide interchange protein DsbA/DsbL / : / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin ...Thioredoxin / Thiol:disulphide interchange protein DsbA/DsbL / : / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesNeisseria meningitidis MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsLafaye, C. / Serre, L.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Biochemical and structural study of the homologues of the thiol-disulfide oxidoreductase DsbA in Neisseria meningitidis.
Authors: Lafaye, C. / Iwema, T. / Carpentier, P. / Jullian-Binard, C. / Kroll, J.S. / Collet, J.F. / Serre, L.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Preliminary crystallographic data of the three homologues of the thiol-disulfide oxidoreductase DsbA in Neisseria meningitidis.
Authors: Lafaye, C. / Iwema, T. / Ferrer, J.L. / Kroll, J.S. / Griat, M. / Serre, L.
History
DepositionJul 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)21,5101
Polymers21,5101
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.080, 46.418, 79.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 21510.436 Da / Num. of mol.: 1 / Fragment: Truncated mature form: UNP residues 41-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Strain: MC58 / Serogroup B / Gene: dsbA-1, NMB0278 / Plasmid: pLIM01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-codon plus-RIL / References: UniProt: Q9K189
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 35.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.4 M Ammonium sulfate, 0.1 M Bicine pH 9.0 or 1.6 M Trisodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
Details: Mirrors, horizontal focusing by sagitally curved 2nd crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→46 Å / Num. obs: 26907 / % possible obs: 99.5 % / Redundancy: 10.2 % / Biso Wilson estimate: 17.4 Å2 / Rsym value: 0.064 / Net I/σ(I): 6.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.241 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XNEMOdata collection
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→20.54 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.247 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21064 1342 5 %RANDOM
Rwork0.18148 ---
obs0.18148 25466 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.808 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 0 179 1711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221570
X-RAY DIFFRACTIONr_bond_other_d0.0010.021053
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.9492133
X-RAY DIFFRACTIONr_angle_other_deg0.85432600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5155202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80825.8973
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92115282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.014154
X-RAY DIFFRACTIONr_chiral_restr0.0690.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021756
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02293
X-RAY DIFFRACTIONr_nbd_refined0.2070.2321
X-RAY DIFFRACTIONr_nbd_other0.1830.21089
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2782
X-RAY DIFFRACTIONr_nbtor_other0.0860.2727
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2113
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.226
X-RAY DIFFRACTIONr_mcbond_it0.9331.51272
X-RAY DIFFRACTIONr_mcbond_other0.1651.5393
X-RAY DIFFRACTIONr_mcangle_it1.10721570
X-RAY DIFFRACTIONr_scbond_it1.993700
X-RAY DIFFRACTIONr_scangle_it2.8384.5558
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 100 -
Rwork0.223 1762 -
obs--95.34 %

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