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- PDB-4h2n: Crystal structure of MHPCO, Y270F mutant -

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Basic information

Entry
Database: PDB / ID: 4h2n
TitleCrystal structure of MHPCO, Y270F mutant
Components2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
KeywordsOXIDOREDUCTASE / FAD-binding motif / Oxygenase / FAD / 3-hydroxypyridine-5-carboxylic acid
Function / homology
Function and homology information


FAD binding / monooxygenase activity
Similarity search - Function
D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / 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
BETA-MERCAPTOETHANOL / FLAVIN-ADENINE DINUCLEOTIDE / 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
Similarity search - Component
Biological speciesRhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 Å
AuthorsKobayashi, J. / Yoshida, H. / Mikami, B. / Hayashi, H. / Kamitori, S. / Yagi, T.
CitationJournal: To be Published
Title: Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
Authors: Kobayashi, J. / Yoshida, H. / Mikami, B. / Hayashi, H. / Kamitori, S. / Yagi, T.
History
DepositionSep 12, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
SupersessionApr 2, 2014ID: 3ALK
Revision 1.1Nov 8, 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_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_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

Downloads & links

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Assembly

Deposited unit
A: 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7384
Polymers41,7821
Non-polymers9563
Water1,69394
1
A: 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
hetero molecules

A: 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
hetero molecules

A: 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
hetero molecules

A: 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,95316
Polymers167,1304
Non-polymers3,82312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)49.438, 131.126, 133.032
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase


Mass: 41782.488 Da / Num. of mol.: 1 / Mutation: Y270F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium loti (bacteria) / Strain: MAFF303099 / Gene: mlr6788 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q988D3, EC: 1.14.12.4
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 8% PEG 8000, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 18939 / % possible obs: 96.5 % / Redundancy: 7 % / Biso Wilson estimate: 29.31 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 10
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 4.8 / Num. unique all: 968 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GMB

3gmb


Resolution: 2.302→37.978 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 24.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2484 953 5.04 %
Rwork0.1979 --
obs0.2004 18925 96.37 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.71 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso max: 93.96 Å2 / Biso mean: 33.5164 Å2 / Biso min: 17.87 Å2
Baniso -1Baniso -2Baniso -3
1-19.5813 Å2-0 Å2-0 Å2
2---12.7065 Å2-0 Å2
3----6.8748 Å2
Refinement stepCycle: LAST / Resolution: 2.302→37.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2874 0 63 94 3031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083007
X-RAY DIFFRACTIONf_angle_d1.3844088
X-RAY DIFFRACTIONf_dihedral_angle_d13.7991092
X-RAY DIFFRACTIONf_chiral_restr0.072444
X-RAY DIFFRACTIONf_plane_restr0.004521
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.302-2.42330.29961440.2239258399
2.4233-2.57510.28861240.22122613100
2.5751-2.77390.28031490.2132637100
2.7739-3.05290.24771510.20942626100
3.0529-3.49440.26281610.20542632100
3.4944-4.40160.23671010.1837208077
4.4016-37.98310.2041230.18280199

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