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- PDB-2gvc: Crystal structure of flavin-containing monooxygenase (FMO)from S.... -

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Basic information

Entry
Database: PDB / ID: 2gvc
TitleCrystal structure of flavin-containing monooxygenase (FMO)from S.pombe and substrate (methimazole) complex
Componentsmonooxygenase
KeywordsOXIDOREDUCTASE / FMO / FAD / methimazole / oxygenase / PSI / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / N,N-dimethylaniline monooxygenase activity / cellular detoxification / FAD binding / NADP binding / endoplasmic reticulum membrane
Similarity search - Function
: / Flavin monooxygenase FMO / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / NAD(P)-binding Rossmann-like domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 1-METHYL-1,3-DIHYDRO-2H-IMIDAZOLE-2-THIONE / HYDROGEN PEROXIDE / Thiol-specific monooxygenase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsEswaramoorthy, S. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Mechanism of action of a flavin-containing monooxygenase.
Authors: Eswaramoorthy, S. / Bonanno, J.B. / Burley, S.K. / Swaminathan, S.
History
DepositionMay 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 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: monooxygenase
B: monooxygenase
D: monooxygenase
E: monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,82120
Polymers200,7184
Non-polymers4,10316
Water9,674537
1
A: monooxygenase
B: monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,41110
Polymers100,3592
Non-polymers2,0528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-32 kcal/mol
Surface area35430 Å2
MethodPISA
2
D: monooxygenase
E: monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,41110
Polymers100,3592
Non-polymers2,0528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-33 kcal/mol
Surface area35520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.700, 84.450, 113.510
Angle α, β, γ (deg.)107.73, 90.76, 106.50
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABDE

#1: Protein
monooxygenase


Mass: 50179.543 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: Q9HFE4

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Non-polymers , 5 types, 553 molecules

#2: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O2
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-MMZ / 1-METHYL-1,3-DIHYDRO-2H-IMIDAZOLE-2-THIONE / METHIMAZOLE


Mass: 114.169 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6N2S / Comment: medication*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG 3350, Ammonium Acetate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. all: 112153 / Num. obs: 112153 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 9.3
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.321 / Num. unique all: 9155 / % possible all: 75.7

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Processing

Software
NameVersionClassification
CBASSdata collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1VQW

1vqw


Resolution: 2.22→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The side chain atoms of GLU 444 were not modeled due to lack of electron density.
RfactorNum. reflectionSelection details
Rfree0.2645 4254 RANDOM
Rwork0.23 --
obs0.23 105205 -
all-105205 -
Refinement stepCycle: LAST / Resolution: 2.22→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13944 0 272 537 14753
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007078
X-RAY DIFFRACTIONc_angle_deg1.38022

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