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- PDB-4ltm: Crystal structures of NADH:FMN oxidoreductase (EMOB) - FMN complex -

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Basic information

Entry
Database: PDB / ID: 4ltm
TitleCrystal structures of NADH:FMN oxidoreductase (EMOB) - FMN complex
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
FLAVIN MONONUCLEOTIDE / NADH-dependent FMN reductase
Similarity search - Component
Biological speciesEDTA-degrading bacterium BNC1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.497 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: 2VZH
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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_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
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)22,1244
Polymers21,1161
Non-polymers1,0093
Water1,63991
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)88,49816
Polymers84,4634
Non-polymers4,03512
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 area16150 Å2
ΔGint-131 kcal/mol
Surface area25390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.270, 101.270, 130.220
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-331-

HOH

21A-337-

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, EC: 1.5.1.42
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 4.56 Å3/Da / Density % sol: 73.05 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.497→47.2 Å / Num. all: 14221 / Num. obs: 14221 / Observed criterion σ(F): 2
Reflection shellHighest resolution: 2.497 Å

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LTD

4ltd


Resolution: 2.497→47.193 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 18.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 1422 10 %RANDOM
Rwork0.1979 ---
obs-14218 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.497→47.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1404 0 67 91 1562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071501
X-RAY DIFFRACTIONf_angle_d1.1492050
X-RAY DIFFRACTIONf_dihedral_angle_d11.87524
X-RAY DIFFRACTIONf_chiral_restr0.069237
X-RAY DIFFRACTIONf_plane_restr0.005256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.497-2.58580.24481390.19591248X-RAY DIFFRACTION99
2.5858-2.68930.22371370.19331235X-RAY DIFFRACTION99
2.6893-2.81170.21541380.17681245X-RAY DIFFRACTION99
2.8117-2.95990.22621390.1821250X-RAY DIFFRACTION99
2.9599-3.14530.20551400.18481256X-RAY DIFFRACTION99
3.1453-3.38810.20251400.17591269X-RAY DIFFRACTION99
3.3881-3.72890.1711430.15551276X-RAY DIFFRACTION100
3.7289-4.26820.16871430.1521287X-RAY DIFFRACTION100
4.2682-5.37630.16521450.15391314X-RAY DIFFRACTION100
5.3763-47.20120.20391580.20281416X-RAY DIFFRACTION99

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