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- PDB-6dnu: Crystal Structure of Neisseria meningitidis DsbD c-terminal domai... -

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Basic information

Entry
Database: PDB / ID: 6dnu
TitleCrystal Structure of Neisseria meningitidis DsbD c-terminal domain in the oxidised form
ComponentsThiol:disulfide interchange protein DsbD
KeywordsOXIDOREDUCTASE / disulphide reductase / Dsb proteins
Function / homology
Function and homology information


protein-disulfide reductase / protein-disulfide reductase [NAD(P)H] activity / cytochrome complex assembly / cell redox homeostasis / electron transfer activity / metal ion binding / plasma membrane
Similarity search - Function
Thiol:disulphide interchange protein DsbD / Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / DsbD gamma / Thiol:disulfide interchange protein DsbD, N-terminal domain / Thiol:disulfide interchange protein DsbD, N-terminal / Cytochrome C biogenesis protein, transmembrane domain / Cytochrome C biogenesis protein transmembrane domain / Thioredoxin-like domain / Thioredoxin-like fold / Thioredoxin ...Thiol:disulphide interchange protein DsbD / Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / DsbD gamma / Thiol:disulfide interchange protein DsbD, N-terminal domain / Thiol:disulfide interchange protein DsbD, N-terminal / Cytochrome C biogenesis protein, transmembrane domain / Cytochrome C biogenesis protein transmembrane domain / Thioredoxin-like domain / Thioredoxin-like fold / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbD
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.283 Å
AuthorsHeras, B. / Smith, R.P. / Paxman, J.J.
Citation
Journal: J. Biol. Chem. / Year: 2018
Title: Structural and biochemical insights into the disulfide reductase mechanism of DsbD, an essential enzyme for neisserial pathogens.
Authors: Smith, R.P. / Mohanty, B. / Mowlaboccus, S. / Paxman, J.J. / Williams, M.L. / Headey, S.J. / Wang, G. / Subedi, P. / Doak, B.C. / Kahler, C.M. / Scanlon, M.J. / Heras, B.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Production, biophysical characterization and initial crystallization studies of the N- and C-terminal domains of DsbD, an essential enzyme in Neisseria meningitidis.
Authors: Smith, R.P. / Whitten, A.E. / Paxman, J.J. / Kahler, C.M. / Scanlon, M.J. / Heras, B.
History
DepositionJun 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 25, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein DsbD
B: Thiol:disulfide interchange protein DsbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3848
Polymers26,6902
Non-polymers1,6946
Water1,04558
1
A: Thiol:disulfide interchange protein DsbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1924
Polymers13,3451
Non-polymers8473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol:disulfide interchange protein DsbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1924
Polymers13,3451
Non-polymers8473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.796, 35.796, 188.738
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Thiol:disulfide interchange protein DsbD / Protein-disulfide reductase / Disulfide reductase


Mass: 13345.065 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (strain alpha14) (bacteria)
Strain: alpha14 / Gene: dsbD, NMO_1340 / Plasmid: pMCSG7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C6S7X6, protein-disulfide reductase
#2: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C12H26O7 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 5% w/v PEG 400, 1.7-2.2 M citrate/citric acid pH 7.0 - 7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 10761 / % possible obs: 99.8 % / Redundancy: 12.5 % / Biso Wilson estimate: 44.65 Å2 / Rmerge(I) obs: 0.115 / Χ2: 1.225 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.28-2.3612.70.55610831.0531100
2.36-2.4612.70.4710481.1031100
2.46-2.5712.80.35311071.1141100
2.57-2.712.80.27410411.1921100
2.7-2.8712.80.21810751.2721100
2.87-3.0912.80.16910761.2371100
3.09-3.4112.70.13110751.31100
3.41-3.912.20.11810851.429199.7
3.9-4.9111.50.09110681.188199.3
4.91-5012.20.07911031.37199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.283→35.796 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 30.37
RfactorNum. reflection% reflection
Rfree0.2569 516 4.82 %
Rwork0.1893 --
obs0.1923 10700 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.15 Å2 / Biso mean: 52.6507 Å2 / Biso min: 27.72 Å2
Refinement stepCycle: final / Resolution: 2.283→35.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 0 45 58 1959
Biso mean--72.28 52.33 -
Num. residues----233
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2834-2.51310.31691390.209425222661100
2.5131-2.87660.31221400.210625262666100
2.8766-3.62370.26141180.214625832701100
3.6237-35.80040.22741190.16922553267299
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)
19.70376.11624.35399.8422.78387.9004-0.0145-0.14960.49460.81740.1078-0.3066-0.51510.064-0.040.46380.1394-0.06790.4102-0.00380.534312.14380.174910.4727
25.04232.0748-3.03873.7824-1.51534.459-0.03080.1234-0.46270.0380.0043-0.33440.177-0.3008-0.01540.31320.0465-0.03020.33960.04260.36687.8547-1.1511-2.3865
34.80162.8084-5.44636.2986-0.76539.54440.27790.0848-0.36030.35870.28930.2636-0.1568-1.0682-0.28120.3980.08820.01040.46890.08810.39560.9033.7490.3432
48.1496-0.5320.38956.2480.62182.5034-0.1420.0011.27090.50550.3089-0-0.4961-0.3726-0.25520.4170.0630.00460.3372-0.03140.50748.721811.3925-1.9956
57.56383.4056-1.0517.2951-4.86173.62340.16450.86670.5625-0.5518-0.1029-0.39270.23340.2459-0.17120.53060.10220.02940.49940.08020.505317.9262-5.491716.0186
63.33031.83691.35215.08311.83794.7098-0.0055-0.16860.40470.3390.03420.24640.09340.02550.00050.34890.0486-0.01960.3122-0.01320.395318.5937-6.832432.9768
73.71144.8035-2.06966.2597-3.2218.2511-0.43550.28070.0001-0.37330.5204-0.17180.0001-0.6242-0.15010.34580.0911-0.03070.45080.00620.477414.2168-9.791224.4008
85.86051.7436-4.66093.9667-0.78817.78830.64032.0974-1.1245-0.7408-0.07150.19231.66860.001-0.25680.55920.0017-0.11950.4918-0.1010.386513.9124-21.444519.8747
94.7032-1.0094-0.60156.7403-3.64738.4433-0.0143-0.2937-0.36370.0492-0.0263-0.03481.02010.1697-0.03690.49890.1043-0.06410.2937-0.0120.430921.7012-17.153525.6407
107.3823-2.2005-3.23488.229-2.19725.83170.2661.1414-0.1974-0.4484-0.2457-0.14240.5971-0.39650.29530.405-0.0153-0.08790.4199-0.05410.368427.3525-12.315126.1462
119.00920.6509-0.67219.1034.77632.6393-0.26690.35820.07210.61190.0548-0.93280.13591.23320.08790.38190.0038-0.03240.42190.05090.596531.142-5.668230.313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 23 )A0 - 23
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 76 )A24 - 76
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 88 )A77 - 88
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 115 )A89 - 115
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 23 )B-1 - 23
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 54 )B24 - 54
7X-RAY DIFFRACTION7chain 'B' and (resid 55 through 67 )B55 - 67
8X-RAY DIFFRACTION8chain 'B' and (resid 68 through 76 )B68 - 76
9X-RAY DIFFRACTION9chain 'B' and (resid 77 through 88 )B77 - 88
10X-RAY DIFFRACTION10chain 'B' and (resid 89 through 103 )B89 - 103
11X-RAY DIFFRACTION11chain 'B' and (resid 104 through 115 )B104 - 115

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