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

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Basic information

Entry
Database: PDB / ID: 6dnl
TitleCrystal Structure of Neisseria meningitidis DsbD c-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 / protein-disulfide reductase activity / membrane => GO:0016020 / cell redox homeostasis / electron transfer activity / 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
ACETATE ION / Thiol:disulfide interchange protein DsbD / Thiol:disulfide interchange protein DsbD
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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 6, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,80112
Polymers13,1011
Non-polymers70011
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-196 kcal/mol
Surface area6850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.250, 28.060, 45.800
Angle α, β, γ (deg.)90.000, 100.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 13100.884 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: dipZ, dsbD, A6L27_07425, ERS514851_00843 / Plasmid: pMCSG7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0Y6T358, UniProt: Q9JYM0*PLUS, protein-disulfide reductase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.2 M zinc acetate dehydrate, 0.1 M sodium cacodylate trihydrate pH 7.5 and 18% w/v PEG 8000

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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: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→44.965 Å / Num. obs: 12150 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 18.71 Å2 / Rpim(I) all: 0.059 / Rrim(I) all: 0.116 / Rsym value: 0.099 / Net I/av σ(I): 5 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.7-1.793.90.5311.417500.3060.6140.53199.9
1.79-1.93.90.3432.216740.20.3980.343100
1.9-2.033.90.2223.315520.130.2580.22299.8
2.03-2.193.90.1624.214700.0940.1880.16299.9
2.19-2.43.80.1275.213390.0730.1470.12799.9
2.4-2.693.80.1046.212260.060.120.10499.9
2.69-3.13.70.0897.310770.0520.1030.08999.5
3.1-3.83.60.0738.29190.0440.0860.07399.8
3.8-5.383.40.0698.77250.0430.0820.069100
5.38-34.2983.60.05312.64180.0310.0620.05399

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALA3.3.22data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→34.298 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.45
RfactorNum. reflection% reflection
Rfree0.2134 634 5.22 %
Rwork0.177 --
obs0.1789 12135 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.14 Å2 / Biso mean: 28.3486 Å2 / Biso min: 9.54 Å2
Refinement stepCycle: final / Resolution: 1.7→34.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms921 0 29 94 1044
Biso mean--35.16 37.75 -
Num. residues----115
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.83130.29191070.236422952402100
1.8313-2.01550.2731160.202222762392100
2.0155-2.30710.191430.175722742417100
2.3071-2.90650.24191410.183822832424100
2.9065-34.30490.18481270.15882373250099
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)
14.71191.01752.29463.64641.8183.6756-0.11220.20210.1191-0.06220.02370.0715-0.05440.06060.09870.10860.00190.02490.10220.02710.07310.27221.35314.4397
24.0442-1.08930.01583.20620.08875.23710.43690.60460.2744-1.1145-0.1591-0.11970.15580.3581-0.07960.4550.01920.01280.30170.06460.232313.54422.025.1998
32.745-0.6572-0.58713.0471.01882.3586-0.036-0.15270.04970.10950.1008-0.14150.16160.2642-0.01810.13210.0173-0.00040.16040.01560.10576.1477-2.134818.3679
47.92094.1904-3.57748.5888-1.64055.9224-0.07560.9047-0.91-0.4341-0.0846-0.4840.98110.16290.22380.37120.1538-0.00950.2988-0.07230.20729.7827-9.70065.1376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 33 )A1 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 54 )A34 - 54
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 103 )A55 - 103
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 115 )A104 - 115

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