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- PDB-3a3t: The oxidoreductase NmDsbA1 from N. meningitidis -

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Basic information

Entry
Database: PDB / ID: 3a3t
TitleThe oxidoreductase NmDsbA1 from N. meningitidis
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / thioredoxin-like / DsbA fold
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 serogroup B (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsVivian, J.P. / Scoullar, J. / Bushell, S. / Beddoe, T. / Wilce, M.C.J. / Byres, E. / Boyle, T.P. / Rimmer, K. / Doak, B. / Simpson, J.S. ...Vivian, J.P. / Scoullar, J. / Bushell, S. / Beddoe, T. / Wilce, M.C.J. / Byres, E. / Boyle, T.P. / Rimmer, K. / Doak, B. / Simpson, J.S. / Graham, B. / Heras, B. / Kahler, C.M. / Rossjohn, J. / Scanlon, M.J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure and function of the oxidoreductase DsbA1 from Neisseria meningitidis
Authors: Vivian, J.P. / Scoullar, J. / Rimmer, K. / Bushell, S.R. / Beddoe, T. / Wilce, M.C.J. / Byres, E. / Boyle, T.P. / Doak, B. / Simpson, J.S. / Graham, B. / Heras, B. / Kahler, C.M. / Rossjohn, J. / Scanlon, M.J.
History
DepositionJun 19, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
E: Thiol:disulfide interchange protein DsbA
F: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)140,9556
Polymers140,9556
Non-polymers00
Water14,844824
1
A: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)23,4921
Polymers23,4921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)23,4921
Polymers23,4921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)23,4921
Polymers23,4921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)23,4921
Polymers23,4921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)23,4921
Polymers23,4921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)23,4921
Polymers23,4921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.208, 59.301, 126.522
Angle α, β, γ (deg.)90.00, 108.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thiol:disulfide interchange protein DsbA / NmDsbA1


Mass: 23492.479 Da / Num. of mol.: 6 / Fragment: NmDsbA3 residues 42-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Strain: serogroup B / Gene: dsbA-1 / Plasmid: pET45b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9K189, protein disulfide-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 824 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 35% PEG 4000, 0.1M MES pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2008 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 67649 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 25
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.5.0088refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZNM

2znm


Resolution: 2.1→48.06 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 12.715 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.24618 3604 5.1 %RANDOM
Rwork0.18944 ---
obs0.19235 67649 98.04 %-
all-73395 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.019 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.03 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9108 0 0 824 9932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0229318
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0711.95212600
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6951158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08326.081444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.275151674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.231524
X-RAY DIFFRACTIONr_chiral_restr0.0540.21386
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217008
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_it0.561.5188
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.032302
X-RAY DIFFRACTIONr_scbond_it1.5023117
X-RAY DIFFRACTIONr_scangle_it2.2354.5115
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 238 -
Rwork0.238 5054 -
obs--99.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.65090.7592-0.20882.6367-1.06221.93170.0812-0.19630.18550.2581-0.04670.0347-0.18950.0711-0.03450.04410.00290.0110.0737-0.04420.067333.01190.4111-31.1087
21.9468-0.6095-0.10042.6780.65442.42870.03890.16440.1584-0.0687-0.0130.0702-0.1571-0.0847-0.02590.0539-0.0010.00840.1060.03170.100110.1779-25.8415-8.5266
31.49910.16220.45652.8860.69542.30140.02610.05670.0595-0.0838-0.0477-0.0363-0.0670.01410.02160.0056-0.00030.00460.03340.02310.04277.8752-10.6313-49.9354
41.33240.02060.22542.4822-1.00072.03280.0399-0.08570.08390.1815-0.0570.1042-0.0844-0.07370.01720.04-0.0080.00970.0708-0.03480.052535.206720.57069.9942
51.6466-0.4687-0.03433.10650.73262.08990.05830.15160.0283-0.2189-0.0755-0.00430.0289-0.09860.01730.0348-0.00160.00470.08250.02610.04079.5634-10.442430.2643
61.92590.9789-0.50752.8738-1.06481.52110.1445-0.37610.20510.3559-0.12130.0205-0.19760.0999-0.02320.0822-0.0121-0.0070.1523-0.04510.075535.00530.404848.4694
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 212
2X-RAY DIFFRACTION2B-4 - 212
3X-RAY DIFFRACTION3C-4 - 212
4X-RAY DIFFRACTION4D-4 - 212
5X-RAY DIFFRACTION5E-4 - 212
6X-RAY DIFFRACTION6F-4 - 212

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