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- PDB-4jy2: Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid... -

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Basic information

Entry
Database: PDB / ID: 4jy2
TitleCrystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, native and unliganded 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
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: 1.935 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 28, 2013Deposition site: RCSB / Processing site: PDBJ
SupersessionApr 2, 2014ID: 3ALH
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)86,33717
Polymers83,5972
Non-polymers2,74015
Water11,476637
1
A: 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2159
Polymers41,7981
Non-polymers1,4168
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)43,1238
Polymers41,7981
Non-polymers1,3247
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.738, 129.364, 89.302
Angle α, β, γ (deg.)90.00, 122.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-529-

HOH

21A-713-

HOH

31A-714-

HOH

41B-710-

HOH

51B-711-

HOH

61B-712-

HOH

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

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Components

#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
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 8% PEG 8000, 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: 1.935→50 Å / Num. obs: 78611 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.81 Å2 / Rmerge(I) obs: 0.099
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.308 / % possible all: 100

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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: 1.935→49.067 Å / Occupancy max: 1 / Occupancy min: 0.12 / SU ML: 0.15 / σ(F): 1.36 / Phase error: 19.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2012 3955 5.03 %Random
Rwork0.1677 ---
obs0.1694 78588 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.22 Å2 / Biso mean: 17.9298 Å2 / Biso min: 5.47 Å2
Refinement stepCycle: LAST / Resolution: 1.935→49.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5750 0 180 637 6567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076177
X-RAY DIFFRACTIONf_angle_d1.4168405
X-RAY DIFFRACTIONf_dihedral_angle_d13.3462271
X-RAY DIFFRACTIONf_chiral_restr0.08905
X-RAY DIFFRACTIONf_plane_restr0.0051066
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9349-1.95850.24431290.1958244892
1.9585-1.98330.26441400.19132673100
1.9833-2.00940.20131430.18452617100
2.0094-2.0370.22061340.18382696100
2.037-2.06610.20041190.18152667100
2.0661-2.09690.25041600.17662649100
2.0969-2.12970.20251450.17472717100
2.1297-2.16460.22571540.17612629100
2.1646-2.20190.22751420.16492653100
2.2019-2.24190.20511650.16572641100
2.2419-2.28510.20791310.16452699100
2.2851-2.33170.20761190.1652640100
2.3317-2.38240.2021420.16432684100
2.3824-2.43780.18741330.16762694100
2.4378-2.49880.22071510.1712663100
2.4988-2.56630.20171540.17622678100
2.5663-2.64190.21451400.17172629100
2.6419-2.72710.20951460.17322684100
2.7271-2.82460.21420.17642676100
2.8246-2.93770.22081440.18082686100
2.9377-3.07130.20371460.1732660100
3.0713-3.23320.20991370.17542669100
3.2332-3.43580.19531430.1672702100
3.4358-3.7010.17351360.15972685100
3.701-4.07320.1891240.15262690100
4.0732-4.66220.16461430.14122687100
4.6622-5.87240.18151430.1492691100
5.8724-49.08250.18451500.17652726100

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