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- PDB-4nwz: Structure of bacterial type II NADH dehydrogenase from Caldalkali... -

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Basic information

Entry
Database: PDB / ID: 4nwz
TitleStructure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum at 2.5A resolution
ComponentsFAD-dependent pyridine nucleotide-disulfide oxidoreductase
KeywordsOXIDOREDUCTASE / Rossmann Fold / Dehydrogenase / Nucleotide binding / Membrane/Cytoplasm
Function / homology
Function and homology information


aerobic electron transport chain / NAD(P)H dehydrogenase (quinone) 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNakatani, Y. / Heikal, A. / Lott, J.S. / Sazanov, L.A. / Baker, E.N. / Cook, G.M.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation.
Authors: Heikal, A. / Nakatani, Y. / Dunn, E. / Weimar, M.R. / Day, C.L. / Baker, E.N. / Lott, J.S. / Sazanov, L.A. / Cook, G.M.
History
DepositionDec 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
B: 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
Water3,837213
1
A: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
B: 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
3
A: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
hetero molecules

B: 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
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area4630 Å2
ΔGint-17 kcal/mol
Surface area34750 Å2
MethodPISA
4
C: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
hetero molecules

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
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area4630 Å2
ΔGint-20 kcal/mol
Surface area34370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.791, 114.477, 130.594
Angle α, β, γ (deg.)90.00, 92.04, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLYGLYAA3 - 3973 - 397
21LYSLYSGLYGLYBB3 - 3973 - 397
12LYSLYSLYSLYSAA3 - 3953 - 395
22LYSLYSLYSLYSCC3 - 3953 - 395
13PROPROLYSLYSAA4 - 3964 - 396
23PROPROLYSLYSDD4 - 3964 - 396
14LYSLYSLYSLYSBB3 - 3953 - 395
24LYSLYSLYSLYSCC3 - 3953 - 395
15PROPROLYSLYSBB4 - 3964 - 396
25PROPROLYSLYSDD4 - 3964 - 396
16PROPROLYSLYSCC4 - 3964 - 396
26PROPROLYSLYSDD4 - 3964 - 396

NCS ensembles :
ID
1
2
3
4
5
6

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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 (bacteria)
Strain: TA2.A1 / 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


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.12M mixture of 1,6-hexanediol,1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol, 0.1M Tris-Bicine pH 8.5, 30% glycerol, PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2013
RadiationMonochromator: SILICON DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.5→65.3 Å / Num. all: 74022 / Num. obs: 73752 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 15.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4 % / Rmerge(I) obs: 0.132 / Mean I/σ(I) obs: 1.1 / Num. unique all: 10759 / Rsym value: 0.132 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G6G

4g6g


Resolution: 2.5→64.61 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.431 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.416 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26864 3717 5 %RANDOM
Rwork0.21696 ---
obs0.21962 70011 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.979 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20.36 Å2
2---0.21 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.5→64.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12005 0 212 213 12430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912179
X-RAY DIFFRACTIONr_bond_other_d0.0040.0211681
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.98816578
X-RAY DIFFRACTIONr_angle_other_deg0.808326786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90451557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12424.382502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.636151929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.961565
X-RAY DIFFRACTIONr_chiral_restr0.070.21876
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02113845
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022652
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_it9.4267.6536227
X-RAY DIFFRACTIONr_mcbond_other9.4277.6526226
X-RAY DIFFRACTIONr_mcangle_it12.55211.4757772
X-RAY DIFFRACTIONr_mcangle_other12.55111.4767773
X-RAY DIFFRACTIONr_scbond_it9.018.0235952
X-RAY DIFFRACTIONr_scbond_other9.018.0225953
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.68111.8098803
X-RAY DIFFRACTIONr_long_range_B_refined15.62862.22414812
X-RAY DIFFRACTIONr_long_range_B_other15.63962.23914782
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: INTERATOMIC DISTANCE / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A229260.1
12B229260.1
21A226750.1
22C226750.1
31A209600.09
32D209600.09
41B231560.09
42C231560.09
51B219650.05
52D219650.05
61C211880.08
62D211880.08
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 279 -
Rwork0.366 5149 -
obs--99.94 %

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