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- PDB-1vqw: Crystal structure of a protein with similarity to flavin-containi... -

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Basic information

Entry
Database: PDB / ID: 1vqw
TitleCrystal structure of a protein with similarity to flavin-containing monooxygenases and to mammalian dimethylalanine monooxygenases
ComponentsPROTEIN WITH SIMILARITY TO FLAVIN-CONTAINING MONOOXYGENASES AND TO MAMMALIAN DIMETHYLALANINE MONOOXYGENASES
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / DIMER / FLAVIN-CONTAINING / NYSGXRC / PROTEIN STRUCTURE INITIATIVE / PSI / T1729 / New York SGX Research Center for Structural Genomics
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 / Thiol-specific monooxygenase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 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
DepositionJan 5, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionJan 11, 2005ID: 1YBP
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN WITH SIMILARITY TO FLAVIN-CONTAINING MONOOXYGENASES AND TO MAMMALIAN DIMETHYLALANINE MONOOXYGENASES
B: PROTEIN WITH SIMILARITY TO FLAVIN-CONTAINING MONOOXYGENASES AND TO MAMMALIAN DIMETHYLALANINE MONOOXYGENASES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8376
Polymers102,7902
Non-polymers2,0484
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-32 kcal/mol
Surface area36730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.590, 72.640, 80.350
Angle α, β, γ (deg.)99.00, 107.09, 102.02
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PROTEIN WITH SIMILARITY TO FLAVIN-CONTAINING MONOOXYGENASES AND TO MAMMALIAN DIMETHYLALANINE MONOOXYGENASES


Mass: 51394.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: Q9HFE4
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 3.2 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: PEG 4000, Ammonium acetate, Sodium citrate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 5.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97920, 0.97940, 0.95000
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 28, 2004
RadiationMonochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.951
ReflectionResolution: 2.4→50 Å / Num. all: 47252 / Num. obs: 47252 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.076 / Net I/σ(I): 8.2
Reflection shellResolution: 2.4→2.49 Å / Num. unique all: 4645 / % possible all: 96.2

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Processing

Software
NameVersionClassification
CBASSdata collection
HKL-2000data reduction
SOLVE& SHARPphasing
CNS1.1refinement
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→50 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1335 -RANDOM
Rwork0.226 ---
obs0.226 44190 92.3 %-
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6980 0 130 382 7492
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006703
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.40935
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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