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- PDB-1nox: NADH OXIDASE FROM THERMUS THERMOPHILUS -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1nox
TitleNADH OXIDASE FROM THERMUS THERMOPHILUS
ComponentsNADH OXIDASE
KeywordsFLAVOENZYME / FLAVOPROTEIN FMN / OXIDOREDUCTASE / THERMOPHILE
Function / homology
Function and homology information


NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase (ubiquinone) activity
Similarity search - Function
NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NADH dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS, MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsHecht, H.J. / Erdmann, H. / Park, H.J. / Sprinzl, M. / Schmid, R.D.
CitationJournal: Nat.Struct.Biol. / Year: 1995
Title: Crystal structure of NADH oxidase from Thermus thermophilus.
Authors: Hecht, H.J. / Erdmann, H. / Park, H.J. / Sprinzl, M. / Schmid, R.D.
History
DepositionNov 20, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADH OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2372
Polymers22,7801
Non-polymers4561
Water1,67593
1
A: NADH OXIDASE
hetero molecules

A: NADH OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4744
Polymers45,5612
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area8030 Å2
ΔGint-39 kcal/mol
Surface area17180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.530, 60.600, 56.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein NADH OXIDASE


Mass: 22780.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PTNADOX / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q60049, NADH dehydrogenase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.4 Å3/Da / Density % sol: 47 %
Crystal growpH: 6
Details: 0.05 M MES-TRIS BUFFER PH 6.0, 26 % PEG 4000, 0.3 M NACL, 50 MM FMN
Crystal grow
*PLUS
Temperature: 12 ℃ / pH: 6.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlNADH oxidase1drop
210 mMFAD1reservoir
30.8 Mammonium sulfate1reservoir
40.1 Mcitrate-pjosphate1reservoir
50.25 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 1.59 Å / Num. obs: 28064 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.069 / Net I/σ(I): 6.2
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.071 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.071 / % possible all: 95.3
Reflection shell
*PLUS
% possible obs: 95.3 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
REFMACrefinement
X-PLORrefinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: ISOMORPHOUS, MOLECULAR REPLACEMENT
Starting model: MODEL FROM ISOMORPHOUS REPLACEMENT

Resolution: 1.59→21 Å / σ(F): 0 / Details: FREE-R-VALUE INTRODUCED LATE IN REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.20432 28064 5 %
Rwork0.1823 --
obs0.1896 28064 96.2 %
Displacement parametersBiso mean: 23.3 Å2
Refine analyzeLuzzati d res low obs: 7 Å / Luzzati sigma a obs: 0.03 Å
Refinement stepCycle: LAST / Resolution: 1.59→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1571 0 31 93 1695
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6512
X-RAY DIFFRACTIONp_mcangle_it2.4233
X-RAY DIFFRACTIONp_scbond_it2.5032
X-RAY DIFFRACTIONp_scangle_it4.0173
X-RAY DIFFRACTIONp_plane_restr0.02450.03
X-RAY DIFFRACTIONp_chiral_restr0.1340.15
X-RAY DIFFRACTIONp_singtor_nbd0.1730.3
X-RAY DIFFRACTIONp_multtor_nbd0.2740.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.17
X-RAY DIFFRACTIONp_staggered_tor1615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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