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- PDB-5wed: Structure of bacterial type II NADH dehydrogenase from Caldalkali... -

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Basic information

Entry
Database: PDB / ID: 5wed
TitleStructure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum at 2.15A resolution
ComponentsFAD-dependent pyridine nucleotide-disulfide oxidoreductase
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD / DEHYDROGENASE / NUCLEOTIDE BINDING / MEMBRANE/CYTOPLASM
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
FAD/NAD(P)-binding domain - #100 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FAD-dependent pyridine nucleotide-disulfide oxidoreductase
Similarity search - Component
Biological speciesCaldalkalibacillus thermarum TA2.A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.15 Å
AuthorsNakatani, Y. / Aragao, D. / Cook, G.M.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Health Research Council (HRC) New Zealand
Maurice Wilkins Centre for Molecular Biodiscovery New Zealand
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of type II NADH:quinone oxidoreductase from Caldalkalibacillus thermarum with an improved resolution of 2.15 angstrom.
Authors: Nakatani, Y. / Jiao, W. / Aragao, D. / Shimaki, Y. / Petri, J. / Parker, E.J. / Cook, G.M.
History
DepositionJul 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 29, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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
B: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
A: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
C: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
D: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,4308
Polymers178,2884
Non-polymers3,1424
Water9,044502
1
B: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
A: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7154
Polymers89,1442
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
D: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7154
Polymers89,1442
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.804, 113.570, 129.781
Angle α, β, γ (deg.)90.00, 91.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FAD-dependent pyridine nucleotide-disulfide oxidoreductase


Mass: 44571.988 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldalkalibacillus thermarum TA2.A1 (bacteria)
Gene: CathTA2_0279 / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: F5L3B8
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 3.07 Å3/Da / Density % sol: 59.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M BICINE/TRIS BUFFER PH8.5 INCLUDING 10% (V/V) PEG 4000, 25% (V/V) ETHYLENE GLYCOL, 150 mM D,L-LYSINE, 10 mM MENADIONE

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.15→48.9 Å / Num. obs: 105403 / % possible obs: 91.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 38.6 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.075 / Net I/σ(I): 17.3
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.696 / Num. unique obs: 5541 / CC1/2: 0.566 / Rpim(I) all: 0.61 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.15→48.867 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.15
RfactorNum. reflection% reflection
Rfree0.2379 5241 4.99 %
Rwork0.2079 --
obs0.2094 105123 91.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→48.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11721 0 212 502 12435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312182
X-RAY DIFFRACTIONf_angle_d0.71616623
X-RAY DIFFRACTIONf_dihedral_angle_d13.5444265
X-RAY DIFFRACTIONf_chiral_restr0.0281921
X-RAY DIFFRACTIONf_plane_restr0.0042129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1501-2.17450.32421430.30863589X-RAY DIFFRACTION98
2.1745-2.20010.32361610.33558X-RAY DIFFRACTION97
2.2001-2.22690.34871020.30192244X-RAY DIFFRACTION89
2.2551-2.28480.3812410.3119551X-RAY DIFFRACTION63
2.2848-2.31610.29121800.27083572X-RAY DIFFRACTION98
2.3161-2.34920.31151890.25933492X-RAY DIFFRACTION97
2.3492-2.38420.27372060.24463584X-RAY DIFFRACTION100
2.3842-2.42150.28711710.24473664X-RAY DIFFRACTION100
2.4215-2.46120.29412140.22973585X-RAY DIFFRACTION100
2.4612-2.50360.2572020.23823592X-RAY DIFFRACTION100
2.5036-2.54910.29981940.2293607X-RAY DIFFRACTION100
2.5491-2.59820.25441830.22393645X-RAY DIFFRACTION100
2.5982-2.65120.26531810.22163612X-RAY DIFFRACTION100
2.6512-2.70880.2681890.22343610X-RAY DIFFRACTION100
2.7088-2.77180.25981850.22923633X-RAY DIFFRACTION100
2.7718-2.84110.2692050.2313583X-RAY DIFFRACTION100
2.8411-2.9180.25361870.22043642X-RAY DIFFRACTION100
2.918-3.00380.24322300.22633594X-RAY DIFFRACTION100
3.0038-3.10070.25441820.21543572X-RAY DIFFRACTION100
3.1007-3.21160.23461890.20923655X-RAY DIFFRACTION100
3.2116-3.34010.21981820.20613646X-RAY DIFFRACTION100
3.3401-3.49210.26271830.20993619X-RAY DIFFRACTION100
3.4921-3.67610.34041800.26843457X-RAY DIFFRACTION95
3.6761-3.90640.23212100.23133526X-RAY DIFFRACTION98
3.9064-4.20780.23311870.18213615X-RAY DIFFRACTION99
4.2078-4.6310.18011900.1563623X-RAY DIFFRACTION99
4.631-5.30040.1921430.16473665X-RAY DIFFRACTION99
5.3004-6.67530.20972270.18823616X-RAY DIFFRACTION99
6.6753-48.87990.16662050.1643531X-RAY DIFFRACTION95
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)
11.21770.63060.28583.04341.16161.1710.0131-0.14230.13480.01610.0823-0.1734-0.0937-0.0055-0.09720.29190.04410.03420.2311-0.00490.26983.711424.210761.8468
22.06110.4020.32772.2171.4422.06630.09980.2052-0.1753-0.2511-0.09320.1418-0.1422-0.2157-0.02980.35060.0141-0.03350.35980.00110.2561-4.2207-6.683828.4711
31.8228-0.0266-0.88620.8460.70782.4807-0.08070.0312-0.3120.0682-0.1540.09160.3361-0.26060.1860.3147-0.071-0.02820.30290.05850.3398-28.911932.1493-3.6651
41.20620.52860.3131.47231.19582.7657-0.0151-0.21760.42510.1217-0.17660.26120.0501-0.06850.14260.3368-0.0733-0.02190.3952-0.03510.4837-22.560759.032733.3773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 396 )
2X-RAY DIFFRACTION2chain 'A' and (resid 3 through 396 )
3X-RAY DIFFRACTION3chain 'C' and (resid 3 through 396 )
4X-RAY DIFFRACTION4chain 'D' and (resid 3 through 396 )

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