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- PDB-2cdu: The Crystal Structure of Water-forming NAD(P)H Oxidase from Lacto... -

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Basic information

Entry
Database: PDB / ID: 2cdu
TitleThe Crystal Structure of Water-forming NAD(P)H Oxidase from Lactobacillus sanfranciscensis
ComponentsNADPH OXIDASE
KeywordsOXIDOREDUCTASE / NAD(P)H OXIDASE / FLAVOENZYME
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
: / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...: / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / NADH oxidase
Similarity search - Component
Biological speciesLACTOBACILLUS SANFRANCISCENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLountos, G.T. / Jiang, R. / Wellborn, W.B. / Thaler, T.L. / Bommarius, A.S. / Orville, A.M.
Citation
Journal: Biochemistry / Year: 2006
Title: The Crystal Structure of Nad(P)H Oxidase from Lactobacillus Sanfranciscensis: Insights Into the Conversion of O(2) Into Two Water Molecules by the Flavoenzyme.
Authors: Lountos, G.T. / Jiang, R. / Wellborn, W.B. / Thaler, T.L. / Bommarius, A.S. / Orville, A.M.
#1: Journal: Acta Crsytallogr, Sect D / Year: 2004
Title: Crystallization and Preliminary Analysis of a Water-Forming Nadh Oxidase from Lactobacillus Sanfranciscensis
Authors: Lountos, G.T. / Riebel, B.R. / Wellborn, W.B. / Bommarius, A.S. / Orville, A.M.
#2: Journal: Adv.Synth.Catal. / Year: 2003
Title: Cofactor Regeneration of Both Nad from Nadh and Nadp from Nadph: Nadh Oxidase from Lactobacillus Sanfranciscensis
Authors: Riebel, B.R. / Gibbs, P.R. / Wellborn, W.B. / Bommarius, A.S.
#3: Journal: Adv.Synth.Catal. / Year: 2002
Title: Cofactor Regeneration of Nad from Nadh: Novel Water-Forming Nadh Oxidases
Authors: Riebel, B.R. / Gibbs, P.R. / Wellborn, W.B. / Bommarius, A.S.
History
DepositionJan 28, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 26, 2022Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _atom_site.label_alt_id / _atom_site.occupancy ..._atom_site.label_alt_id / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH OXIDASE
B: NADPH OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8666
Polymers99,4402
Non-polymers2,4264
Water12,755708
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.636, 92.644, 163.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NADPH OXIDASE


Mass: 49720.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOBACILLUS SANFRANCISCENSIS (bacteria)
Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HB101
References: UniProt: Q9F1X5, Oxidoreductases; Acting on NADH or NADPH
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.3 Å3/Da / Density % sol: 45.5 %
Crystal growpH: 7
Details: 10 MG/ML PROTEIN, 100MM HEPES PH 7.0, 18% W/V PEG 4000, 8% V/V 2-PROPANOL, 20 MM DITHIOTHREITOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9997
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9997 Å / Relative weight: 1
ReflectionResolution: 1.8→46.4 Å / Num. obs: 81507 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 29
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.9 / % possible all: 73.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F8W

1f8w


Resolution: 1.8→81.65 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.176 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A 452, B 450, B451, B452 WERE NOT VISIBLE IN THE ELECTRON DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 4054 5 %RANDOM
Rwork0.178 ---
obs0.18 77370 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å20 Å2
2---0.11 Å20 Å2
3----1.98 Å2
Refinement stepCycle: LAST / Resolution: 1.8→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6937 0 160 708 7805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227265
X-RAY DIFFRACTIONr_bond_other_d0.0020.026405
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9889873
X-RAY DIFFRACTIONr_angle_other_deg0.992315000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5425894
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.21140
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027965
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021298
X-RAY DIFFRACTIONr_nbd_refined0.2290.21517
X-RAY DIFFRACTIONr_nbd_other0.2490.27964
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.24275
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2577
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2910.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.811.54473
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49227234
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.37832792
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9354.52639
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 216
Rwork0.303 4188

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