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- PDB-4ltd: Crystal structures of NADH:FMN oxidoreductase (EMOB) - apo form -

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Basic information

Entry
Database: PDB / ID: 4ltd
TitleCrystal structures of NADH:FMN oxidoreductase (EMOB) - apo form
ComponentsNADH-dependent FMN reductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


FMN reductase [NAD(P)H] activity / alkanesulfonate catabolic process / nucleotide binding
Similarity search - Function
NADPH-dependent FMN reductase, SsuE / : / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / NADH-dependent FMN reductase
Similarity search - Component
Biological speciesEDTA-degrading bacterium BNC1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.186 Å
AuthorsNissen, M.S. / Youn, B. / Knowles, B.D. / Ballinger, J.W. / Jun, S. / Belchik, S.M. / Xun, L. / Kang, C.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structures of NADH:FMN oxidoreductase (EmoB) at different stages of catalysis.
Authors: Nissen, M.S. / Youn, B. / Knowles, B.D. / Ballinger, J.W. / Jun, S.Y. / Belchik, S.M. / Xun, L. / Kang, C.
History
DepositionJul 23, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionAug 7, 2013ID: 2VZF
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: NADH-dependent FMN reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4995
Polymers21,1161
Non-polymers3834
Water2,090116
1
A: NADH-dependent FMN reductase
hetero molecules

A: NADH-dependent FMN reductase
hetero molecules

A: NADH-dependent FMN reductase
hetero molecules

A: NADH-dependent FMN reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,99520
Polymers84,4634
Non-polymers1,53316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area12510 Å2
ΔGint-228 kcal/mol
Surface area25970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.925, 100.925, 129.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-346-

HOH

21A-400-

HOH

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Components

#1: Protein NADH-dependent FMN reductase / EmoB


Mass: 21115.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EDTA-degrading bacterium BNC1 (bacteria)
Gene: emoB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F9T2, FMN reductase (NADH)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.51 Å3/Da / Density % sol: 72.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 mg/mL EmoB in 20 mM sodium acetate, pH 5, 1 mM EDTA, 1 mM DTT mixed with an equal volume of reservoir solution (0.1 M MES, pH 6.5, 1.6 M ammonium sulfate, 10% dioxane), VAPOR DIFFUSION, ...Details: 10 mg/mL EmoB in 20 mM sodium acetate, pH 5, 1 mM EDTA, 1 mM DTT mixed with an equal volume of reservoir solution (0.1 M MES, pH 6.5, 1.6 M ammonium sulfate, 10% dioxane), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0332, 0.97925, 0.97942, 0.91162
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2007
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.979251
30.979421
40.911621
ReflectionResolution: 2.186→24.241 Å / Num. all: 36423 / Num. obs: 17012 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.186 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
X-PLORmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
CrystalCleardata reduction
CrystalCleardata scaling
X-PLORphasing
RefinementMethod to determine structure: MAD / Resolution: 2.186→24.241 Å / SU ML: 0.18 / σ(F): 4.1 / Phase error: 15.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1918 1702 10 %RANDOM
Rwork0.1685 ---
obs0.1708 17012 81.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.186→24.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1404 0 20 116 1540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091456
X-RAY DIFFRACTIONf_angle_d1.1671981
X-RAY DIFFRACTIONf_dihedral_angle_d11.744517
X-RAY DIFFRACTIONf_chiral_restr0.08232
X-RAY DIFFRACTIONf_plane_restr0.005252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.186-2.25070.22061000.1666903X-RAY DIFFRACTION59
2.2507-2.32330.17621100.1652987X-RAY DIFFRACTION66
2.3233-2.40620.21041160.17011044X-RAY DIFFRACTION68
2.4062-2.50250.17951220.16551101X-RAY DIFFRACTION72
2.5025-2.61620.19851330.17361195X-RAY DIFFRACTION78
2.6162-2.7540.18991420.17621277X-RAY DIFFRACTION83
2.754-2.92630.19321470.17841325X-RAY DIFFRACTION86
2.9263-3.15180.21431540.17791387X-RAY DIFFRACTION89
3.1518-3.46810.17731580.17091421X-RAY DIFFRACTION91
3.4681-3.96810.17991680.15331504X-RAY DIFFRACTION95
3.9681-4.99210.16711700.14381539X-RAY DIFFRACTION96
4.9921-24.24290.22451820.19531627X-RAY DIFFRACTION95

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