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- PDB-6dnv: Crystal Structure of Neisseria meningitidis DsbD n-terminal domai... -

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Basic information

Entry
Database: PDB / ID: 6dnv
TitleCrystal Structure of Neisseria meningitidis DsbD n-terminal domain in the reduced 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:disulfide interchange protein DsbD, N-terminal domain / 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 ...Thiol:disulfide interchange protein DsbD, N-terminal domain / 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 domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
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: 1.603 Å
AuthorsSmith, R.P. / Heras, B. / 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 8, 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 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)27,8394
Polymers27,6472
Non-polymers1922
Water6,720373
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A: Thiol:disulfide interchange protein DsbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0153
Polymers13,8231
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol:disulfide interchange protein DsbD


Theoretical massNumber of molelcules
Total (without water)13,8231
Polymers13,8231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.980, 116.980, 45.790
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

21A-495-

HOH

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Components

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


Mass: 13823.304 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 2.5 M ammonium sulfate, 0.1 M Tris pH 9.1

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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: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.603→101.308 Å / Num. obs: 47439 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 17.41 Å2 / Rpim(I) all: 0.046 / Rrim(I) all: 0.15 / Rsym value: 0.143 / Net I/av σ(I): 4.2 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.603-1.6910.51.8320.469070.5941.9271.832100
1.69-1.7910.81.0480.764790.3351.1011.048100
1.79-1.9210.70.5431.361230.1740.5710.543100
1.92-2.0710.70.2922.557070.0940.3060.292100
2.07-2.2710.70.1943.852320.0620.2040.194100
2.27-2.5310.70.145.347780.0450.1470.14100
2.53-2.9310.70.1016.842300.0320.1060.101100
2.93-3.5810.60.0896.635800.0290.0940.089100
3.58-5.0710.10.0669.528120.0220.0690.066100
5.07-41.72610.70.04613.215910.0150.0480.04699.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.22data scaling
PHASERphasing
PHENIXdev_1951refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.603→41.726 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.26
RfactorNum. reflection% reflection
Rfree0.1972 2256 4.76 %
Rwork0.1721 --
obs0.1732 47425 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.97 Å2 / Biso mean: 25.0461 Å2 / Biso min: 8.06 Å2
Refinement stepCycle: final / Resolution: 1.603→41.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 10 373 2321
Biso mean--39.96 36.93 -
Num. residues----248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062002
X-RAY DIFFRACTIONf_angle_d1.0592727
X-RAY DIFFRACTIONf_chiral_restr0.049280
X-RAY DIFFRACTIONf_plane_restr0.005367
X-RAY DIFFRACTIONf_dihedral_angle_d12.97723
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6031-1.6380.32751460.275328172963
1.638-1.67610.25361040.255328112915
1.6761-1.7180.25961230.243528332956
1.718-1.76440.23991400.227528022942
1.7644-1.81640.23691720.196127412913
1.8164-1.8750.19181440.185228102954
1.875-1.9420.20221440.170927872931
1.942-2.01980.19111500.158228082958
2.0198-2.11170.18371480.165327862934
2.1117-2.2230.18721300.163928212951
2.223-2.36230.20911650.170828142979
2.3623-2.54460.19191180.172828482966
2.5446-2.80070.19331480.175728132961
2.8007-3.20580.23011120.17928652977
3.2058-4.03840.16091540.146828673021
4.0384-41.74010.18281580.153229463104
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)
10.5516-0.2476-0.16080.461-0.30310.430.03940.0230.079-0.1096-0.0111-0.01430.01730.0454-0.00850.13880.0044-0.01250.05050.00130.1034242.93190.087366.2906
20.073-0.0074-0.15990.0923-0.03210.3984-0.1001-0.11190.09290.21410.0071-0.13530.01020.179-0.00610.17080.0392-0.01460.09880.01520.1122249.480784.600980.8557
30.3573-0.0135-0.04640.06490.00630.02740.10710.08370.12-0.1962-0.1349-0.06870.0943-0.02850.03020.24240.0463-0.02470.1030.0090.1326245.937587.602458.5695
40.1364-0.0849-0.23070.35180.05020.31510.03790.02630.0245-0.10710.01340.0455-0.0229-0.15280.00220.17470.0035-0.01820.09170.00550.1125237.141289.830265.0286
50.01060.00220.01380.00350.02780.15720.0424-0.15540.00590.3373-0.105-0.2828-0.26460.325-0.00020.41660.0261-0.13380.2128-0.00110.3234233.272481.866582.484
60.02050.0144-0.03110.1075-0.00760.06170.110.1955-0.048-0.16160.07010.09030.05150.05370.02950.1479-0.0353-0.06020.12120.00210.2116217.574881.941971.5947
70.69060.2669-0.04990.28620.02090.0130.1624-0.13580.11260.0369-0.07990.38190.1172-0.09920.01010.1442-0.0432-0.05320.0734-0.0020.2013215.815988.355575.0105
80.3670.05380.17650.01720.07370.3086-0.20460.33220.3325-0.48330.17760.2539-0.12090.05070.09410.4303-0.1329-0.13520.24910.09560.2814215.090793.491959.503
90.6926-0.0361-0.45020.1789-0.17620.52690.0402-0.28850.27350.1133-0.09220.2899-0.18240.0235-0.28120.1671-0.01710.03380.0875-0.07580.2626219.398397.632680.4421
101.28870.1562-0.23030.0807-0.11370.18930.0563-0.19920.4111-0.0763-0.04480.3583-0.1373-0.0080.0720.1746-0.0072-0.01160.0564-0.03640.2621214.95293.382977.5661
110.0009-0.0033-0.00170.2205-0.02730.0058-0.14240.10060.1716-0.09890.03980.0745-0.06940.0009-0.13040.6353-0.1489-0.28050.30880.14670.4704207.707189.401653.8204
120.2636-0.0546-0.20810.54390.11270.2057-0.03930.07570.0605-0.15380.16030.11910.0729-0.03790.13120.2082-0.1049-0.05010.13070.02540.1253220.814588.509367.2386
130.41220.1686-0.10660.0797-0.06390.06030.0666-0.3456-0.02870.2015-0.2334-0.0476-0.0693-0.1482-0.01630.1877-0.025-0.02650.1452-0.0030.1598229.534689.74280.1804
140.0144-0.02790.03730.0572-0.07290.0913-0.00890.07240.0317-0.08620.1414-0.14430.01590.05740.17410.2361-0.2527-0.10790.1452-0.06930.1115220.158783.815162.435
150.4596-0.1759-0.50910.07320.18860.5667-0.1273-0.07470.0317-0.25740.0930.2357-0.04040.1708-0.0820.1935-0.0773-0.04820.17270.02540.1489212.481378.550963.0088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 57 )A1 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 70 )A58 - 70
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 88 )A71 - 88
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 123 )A89 - 123
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 6 )B-1 - 6
6X-RAY DIFFRACTION6chain 'B' and (resid 7 through 18 )B7 - 18
7X-RAY DIFFRACTION7chain 'B' and (resid 19 through 38 )B19 - 38
8X-RAY DIFFRACTION8chain 'B' and (resid 39 through 51 )B39 - 51
9X-RAY DIFFRACTION9chain 'B' and (resid 52 through 65 )B52 - 65
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 80 )B66 - 80
11X-RAY DIFFRACTION11chain 'B' and (resid 81 through 88 )B81 - 88
12X-RAY DIFFRACTION12chain 'B' and (resid 89 through 99 )B89 - 99
13X-RAY DIFFRACTION13chain 'B' and (resid 100 through 107 )B100 - 107
14X-RAY DIFFRACTION14chain 'B' and (resid 108 through 114 )B108 - 114
15X-RAY DIFFRACTION15chain 'B' and (resid 115 through 123 )B115 - 123

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