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- PDB-4gf7: Crystal structure of 2-Methyl-3-hydroxypyridine-5-carboxylic acid... -

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Basic information

Entry
Database: PDB / ID: 4gf7
TitleCrystal structure of 2-Methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO), unliganded form
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 / DI(HYDROXYETHYL)ETHER / 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.581 Å
AuthorsKobayashi, J. / Yoshida, H. / Mikami, B. / Hayashi, H. / Kamitori, S. / Sawa, Y. / 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. / Sawa, Y. / Yagi, T.
History
DepositionAug 3, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)43,2299
Polymers41,7981
Non-polymers1,4308
Water7,909439
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)172,91536
Polymers167,1944
Non-polymers5,72132
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_454-x-1,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
Unit cell
Length a, b, c (Å)49.363, 131.287, 132.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-655-

HOH

21A-720-

HOH

31A-932-

HOH

41A-937-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 41798.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: mlr6788 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q988D3, EC: 1.14.12.4

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Non-polymers , 5 types, 447 molecules

#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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.56 Å3/Da / Density % sol: 52.03 %
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: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 55795 / % possible obs: 94.6 % / Redundancy: 8.5 % / Biso Wilson estimate: 12.31 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.3
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 6.1 / % possible all: 95.5

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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: Selenomethionine substitution of the same enzyme

Resolution: 1.581→41.548 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.12 / σ(F): 1.34 / Phase error: 18.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 2829 5.07 %
Rwork0.1647 --
obs0.1661 55773 94.31 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.334 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 64.38 Å2 / Biso mean: 15.7113 Å2 / Biso min: 5.93 Å2
Baniso -1Baniso -2Baniso -3
1-5.4619 Å2-0 Å20 Å2
2---3.6495 Å2-0 Å2
3----1.8124 Å2
Refinement stepCycle: LAST / Resolution: 1.581→41.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2875 0 94 439 3408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063109
X-RAY DIFFRACTIONf_angle_d1.394227
X-RAY DIFFRACTIONf_dihedral_angle_d14.1371159
X-RAY DIFFRACTIONf_chiral_restr0.082455
X-RAY DIFFRACTIONf_plane_restr0.005537
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5814-1.60870.24251420.19132534267691
1.6087-1.63790.20921340.17222623275795
1.6379-1.66940.22051600.1722599275995
1.6694-1.70350.19991440.16862612275694
1.7035-1.74060.18851230.16072664278795
1.7406-1.7810.19271370.15212612274994
1.781-1.82560.19741440.15742612275693
1.8256-1.87490.19861260.16052594272094
1.8749-1.93010.20331320.16252618275093
1.9301-1.99240.19361340.17382581271593
1.9924-2.06360.22881380.17022593273192
2.0636-2.14620.2161280.17012566269492
2.1462-2.24390.20851440.16762563270791
2.2439-2.36220.18621400.17642508264890
2.3622-2.51020.20841420.17642525266791
2.5102-2.7040.19651390.1692658279794
2.704-2.9760.16931520.17732769292198
2.976-3.40650.19421510.159928412992100
3.4065-4.29110.17241620.149528673029100
4.2911-41.56230.17461570.158130053162100

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