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- PDB-2znm: Oxidoreductase NmDsbA3 from Neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 2znm
TitleOxidoreductase NmDsbA3 from Neisseria meningitidis
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / Thioredoxin fold / DsbA-like
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 / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsVivian, J.P. / Scoullar, J. / Robertson, A.L. / Bottomley, S.P. / Horne, J. / Chin, Y. / Velkov, T. / Wielens, J. / Thompson, P.E. / Piek, S. ...Vivian, J.P. / Scoullar, J. / Robertson, A.L. / Bottomley, S.P. / Horne, J. / Chin, Y. / Velkov, T. / Wielens, J. / Thompson, P.E. / Piek, S. / Byres, E. / Beddoe, T. / Wilce, M.C.J. / Kahler, C. / Rossjohn, J. / Scanlon, M.J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural and Biochemical Characterization of the Oxidoreductase NmDsbA3 from Neisseria meningitidis
Authors: Vivian, J.P. / Scoullar, J. / Robertson, A.L. / Bottomley, S.P. / Horne, J. / Chin, Y. / Wielens, J. / Thompson, P.E. / Velkov, T. / Piek, S. / Byres, E. / Beddoe, T. / Wilce, M.C. / Kahler, ...Authors: Vivian, J.P. / Scoullar, J. / Robertson, A.L. / Bottomley, S.P. / Horne, J. / Chin, Y. / Wielens, J. / Thompson, P.E. / Velkov, T. / Piek, S. / Byres, E. / Beddoe, T. / Wilce, M.C. / Kahler, C.M. / Rossjohn, J. / Scanlon, M.J.
History
DepositionApr 30, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein DsbA
B: Thiol:disulfide interchange protein DsbA
C: Thiol:disulfide interchange protein DsbA
D: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)88,7044
Polymers88,7044
Non-polymers00
Water3,171176
1
A: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)22,1761
Polymers22,1761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)22,1761
Polymers22,1761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)22,1761
Polymers22,1761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)22,1761
Polymers22,1761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-34.5 kcal/mol
Surface area34740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.469, 88.531, 84.295
Angle α, β, γ (deg.)90.00, 106.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thiol:disulfide interchange protein DsbA


Mass: 22176.006 Da / Num. of mol.: 4 / Fragment: DsbA3, UNP residues 20-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Strain: serogroup B / Gene: dsbA-3, NMB0407 / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9K0Z4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG4000, 0.1M Tris, pH8.0, 0.2M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97939 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 34110 / % possible obs: 94 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 42 Å2 / Rsym value: 0.048 / Net I/σ(I): 43.3
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 5 / Rsym value: 0.278 / % possible all: 65

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 19.039 / SU ML: 0.231 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.479 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26338 1708 5.3 %RANDOM
Rwork0.20628 ---
obs0.20927 30543 94.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.626 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.41 Å2
2--0.19 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5863 0 0 176 6039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225991
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.9688080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.485736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.923.829269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.613151076
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.661537
X-RAY DIFFRACTIONr_chiral_restr0.0790.2876
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024497
X-RAY DIFFRACTIONr_nbd_refined0.2010.22664
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24009
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.28
X-RAY DIFFRACTIONr_mcbond_it0.6061.53776
X-RAY DIFFRACTIONr_mcangle_it0.80325875
X-RAY DIFFRACTIONr_scbond_it1.49832517
X-RAY DIFFRACTIONr_scangle_it2.0554.52205
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 92 -
Rwork0.26 1639 -
obs--69.07 %

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