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- PDB-4r81: NAD(P)H:quinone oxidoreductase from Methanothermobacter marburgensis -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4r81
TitleNAD(P)H:quinone oxidoreductase from Methanothermobacter marburgensis
ComponentsNADH dehydrogenase
KeywordsOXIDOREDUCTASE / flavodoxin-like/fold / FMN / NAD
Function / homology
Function and homology information


NAD(P)H dehydrogenase (quinone) activity / nucleotide binding / cytosol
Similarity search - Function
: / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Predicted NADH dehydrogenase
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsUllmann, E. / Tan, T.C. / Herwig, C. / Divne, C. / Spadiut, O.
CitationJournal: Biosci.Rep. / Year: 2014
Title: A novel cytosolic NADH:quinone oxidoreductase from Methanothermobacter marburgensis.
Authors: Ullmann, E. / Tan, T.C. / Gundinger, T. / Herwig, C. / Divne, C. / Spadiut, O.
History
DepositionAug 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADH dehydrogenase
B: NADH dehydrogenase
C: NADH dehydrogenase
D: NADH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1118
Polymers94,2864
Non-polymers1,8254
Water7,674426
1
A: NADH dehydrogenase
B: NADH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0564
Polymers47,1432
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-29 kcal/mol
Surface area16650 Å2
MethodPISA
2
C: NADH dehydrogenase
D: NADH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0564
Polymers47,1432
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-28 kcal/mol
Surface area16480 Å2
MethodPISA
3
A: NADH dehydrogenase
B: NADH dehydrogenase
hetero molecules

C: NADH dehydrogenase
D: NADH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1118
Polymers94,2864
Non-polymers1,8254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area13480 Å2
ΔGint-67 kcal/mol
Surface area29650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.998, 94.686, 72.126
Angle α, β, γ (deg.)90.00, 93.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NADH dehydrogenase


Mass: 23571.502 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter marburgensis (archaea)
Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg / Gene: MTBMA_c07320 / Plasmid: pET21d+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D9PVS9
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M NaCl, 0.1 M Bis-Tris, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2014 / Details: mirrors
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.5→47.34 Å / Num. all: 120455 / Num. obs: 120455 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.5→1.6 Å / % possible all: 97.4

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Processing

Software
NameVersionClassification
GDAdata collection
PHASER(PHENIX)phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LCM

3lcm


Resolution: 1.5→45.967 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 1993 1.65 %RANDOM
Rwork0.1655 ---
all0.1662 120454 --
obs0.1662 120454 98.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→45.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6354 0 124 426 6904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066703
X-RAY DIFFRACTIONf_angle_d1.0129084
X-RAY DIFFRACTIONf_dihedral_angle_d14.1542474
X-RAY DIFFRACTIONf_chiral_restr0.072934
X-RAY DIFFRACTIONf_plane_restr0.0041168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.37151400.29318258X-RAY DIFFRACTION97
1.5375-1.57910.2651420.2438353X-RAY DIFFRACTION98
1.5791-1.62560.24411390.20898364X-RAY DIFFRACTION98
1.6256-1.6780.25871500.19468340X-RAY DIFFRACTION98
1.678-1.7380.23981310.17898413X-RAY DIFFRACTION98
1.738-1.80760.26981470.17768430X-RAY DIFFRACTION99
1.8076-1.88990.21021410.15868460X-RAY DIFFRACTION99
1.8899-1.98950.20961460.15458453X-RAY DIFFRACTION99
1.9895-2.11420.20061310.15758532X-RAY DIFFRACTION99
2.1142-2.27740.21541520.15238517X-RAY DIFFRACTION100
2.2774-2.50660.19421350.15718542X-RAY DIFFRACTION100
2.5066-2.86920.21361490.17268572X-RAY DIFFRACTION100
2.8692-3.61470.19181480.16628592X-RAY DIFFRACTION100
3.6147-45.98850.17521420.15058635X-RAY DIFFRACTION99

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