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

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Basic information

Entry
Database: PDB / ID: 3all
TitleCrystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, mutant Y270A
Components2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
KeywordsOXIDOREDUCTASE / alpha/beta fold
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: 1.78 Å
AuthorsKobayashi, J. / Yoshida, H. / Yoshikane, Y. / 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. / Yoshikane, Y. / Kamitori, S. / Yagi, T.
History
DepositionAug 4, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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
B: 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,60111
Polymers83,4132
Non-polymers2,1889
Water6,161342
1
A: 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8466
Polymers41,7061
Non-polymers1,1405
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)42,7545
Polymers41,7061
Non-polymers1,0484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.085, 284.981, 123.683
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
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: 41706.395 Da / Num. of mol.: 2 / Mutation: Y270A
Source method: isolated from a genetically manipulated source
Details: coexpression with chaperonine GroEL ES / 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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 3.02 Å3/Da / Density % sol: 59.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
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 1, 2009
RadiationMonochromator: Si-single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 95547 / Num. obs: 95547 / % possible obs: 98.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.6
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.391 / Num. unique all: 4584 / % possible all: 96.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ALH

3alh
PDB Unreleased entry


Resolution: 1.78→33.78 Å / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 4767 -RANDOM
Rwork0.1959 ---
all0.198 96976 --
obs0.198 95466 98.443 %-
Displacement parametersBiso mean: 22.506 Å2
Baniso -1Baniso -2Baniso -3
1-0.002 Å20 Å20 Å2
2--0.002 Å20 Å2
3----0.004 Å2
Refinement stepCycle: LAST / Resolution: 1.78→33.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5740 0 144 342 6226
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.028
X-RAY DIFFRACTIONr_angle_refined_deg2.206
LS refinement shellResolution: 1.78→1.826 Å
RfactorNum. reflection% reflection
Rfree0.347 339 -
Rwork0.299 --
obs--96.43 %

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