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- PDB-4jy3: Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid... -

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Basic information

Entry
Database: PDB / ID: 4jy3
TitleCrystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5-pyridoxic acid bound form
Components2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
KeywordsOXIDOREDUCTASE / Flavoenzyme / FAD binding motif / 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
Chem-5PR / BETA-MERCAPTOETHANOL / FLAVIN-ADENINE DINUCLEOTIDE / 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsKobayashi, J. / Yoshida, H. / Kamitori, S. / Hayashi, H. / Mizutani, K. / Takahashi, N. / Mikami, B. / Yagi, T.
CitationJournal: To be Published
Title: Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
Authors: Kobayashi, J. / Yoshida, H. / Kamitori, S. / Hayashi, H. / Mizutani, K. / Takahashi, N. / Mikami, B. / Yagi, T.
History
DepositionMar 29, 2013Deposition site: RCSB / Processing site: PDBJ
SupersessionApr 2, 2014ID: 3ALI, 4H28
Revision 1.0Apr 2, 2014Provider: 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

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


Theoretical massNumber of molelcules
Total (without water)86,48917
Polymers83,5972
Non-polymers2,89315
Water16,772931
1
A: 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2148
Polymers41,7981
Non-polymers1,4157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2769
Polymers41,7981
Non-polymers1,4778
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.446, 129.526, 89.565
Angle α, β, γ (deg.)90.00, 122.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-586-

HOH

21A-662-

HOH

31A-796-

HOH

41A-922-

HOH

51B-654-

HOH

61B-687-

HOH

71B-763-

HOH

DetailsBIOLOGICAL UNIT IS TETRAMER, BUT SPECIFIC INTERACTION FOR FORMING TETRAMER IS NOT OBSERVED.

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 41798.488 Da / Num. of mol.: 2
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 , 6 types, 946 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-5PR / 5-hydroxy-4-(hydroxymethyl)-6-methylpyridine-3-carboxylic acid / 5-Pyridoxic acid


Mass: 183.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9NO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 931 / 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: 3.25 Å3/Da / Density % sol: 62.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 8% PEG 8000, 0.5mM 5-pyridoxic acid, 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 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 103436 / % possible obs: 99.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.082
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.315 / % possible all: 95.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→41.822 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.14 / σ(F): 1.35 / Phase error: 17.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1788 5173 5 %Random
Rwork0.1554 ---
obs0.1566 103425 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.9 Å2 / Biso mean: 16.9093 Å2 / Biso min: 5.11 Å2
Refinement stepCycle: LAST / Resolution: 1.77→41.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5750 0 192 931 6873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086237
X-RAY DIFFRACTIONf_angle_d1.4398487
X-RAY DIFFRACTIONf_dihedral_angle_d13.8432294
X-RAY DIFFRACTIONf_chiral_restr0.087906
X-RAY DIFFRACTIONf_plane_restr0.0061078
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7699-1.790.24081610.2056297091
1.79-1.81110.22931830.1952325499
1.8111-1.83310.22851570.19113225100
1.8331-1.85630.2251710.18193381100
1.8563-1.88080.23681680.17663219100
1.8808-1.90650.21371770.17563286100
1.9065-1.93380.20951750.1663274100
1.9338-1.96260.17341740.16553281100
1.9626-1.99330.1981600.16953309100
1.9933-2.0260.20021800.15453256100
2.026-2.06090.16991810.15933245100
2.0609-2.09840.2051610.15453292100
2.0984-2.13870.18291690.15683306100
2.1387-2.18240.17891820.14893263100
2.1824-2.22990.20811710.15133262100
2.2299-2.28170.17891790.15843277100
2.2817-2.33880.16761860.15213232100
2.3388-2.4020.1461740.14943313100
2.402-2.47270.19061800.15343269100
2.4727-2.55250.20551750.15553313100
2.5525-2.64370.1881700.15193261100
2.6437-2.74950.17391660.15343317100
2.7495-2.87460.16741770.15423279100
2.8746-3.02610.18811740.15933309100
3.0261-3.21570.16891690.1563282100
3.2157-3.46390.17151750.15653284100
3.4639-3.81220.17461740.14183308100
3.8122-4.36340.14091580.14153313100
4.3634-5.49540.13211720.13453311100
5.4954-41.83370.1871740.16163361100

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