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- PDB-4h2r: Structure of MHPCO Y270F mutant, 5-hydroxynicotinic acid complex -

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Basic information

Entry
Database: PDB / ID: 4h2r
TitleStructure of MHPCO Y270F mutant, 5-hydroxynicotinic acid complex
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
5-hydroxypyridine-3-carboxylic acid / 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: 2.473 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 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
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
B: 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,81411
Polymers83,5652
Non-polymers2,2499
Water1,45981
1
A: 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
B: 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
hetero molecules

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)171,62822
Polymers167,1304
Non-polymers4,49818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)56.891, 284.553, 125.001
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 41782.488 Da / Num. of mol.: 2 / 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

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Non-polymers , 5 types, 90 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.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-5HN / 5-hydroxypyridine-3-carboxylic acid / 5-Hydroxynicotinic Acid


Mass: 139.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 81 / 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: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 8% PEG 8000, 0.1M Tris-HCl, 10mM 5-Hydroxynicotinic acid, 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: 2.36→50 Å / Num. obs: 40356 / % possible obs: 95.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.8
Reflection shellResolution: 2.36→2.4 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 5.8 / Num. unique all: 1897 / % possible all: 91.5

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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: PDB ENTRY 3GMB

3gmb


Resolution: 2.473→46.953 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 29.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2612 1761 4.96 %
Rwork0.2069 --
obs0.2095 35487 96.25 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 16.167 Å2 / ksol: 0.305 e/Å3
Displacement parametersBiso max: 99.01 Å2 / Biso mean: 45.6828 Å2 / Biso min: 21.49 Å2
Baniso -1Baniso -2Baniso -3
1-28.0428 Å2-0 Å2-0 Å2
2---17.2458 Å2-0 Å2
3----10.7971 Å2
Refinement stepCycle: LAST / Resolution: 2.473→46.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5730 0 150 81 5961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086016
X-RAY DIFFRACTIONf_angle_d1.5138180
X-RAY DIFFRACTIONf_dihedral_angle_d14.5822180
X-RAY DIFFRACTIONf_chiral_restr0.08886
X-RAY DIFFRACTIONf_plane_restr0.0061042
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4734-2.54030.3602950.2834176568
2.5403-2.6150.35151400.2826258297
2.615-2.69940.40341410.2844259297
2.6994-2.79590.35621310.2523259498
2.7959-2.90780.30811280.2478261797
2.9078-3.04020.28071220.2355261598
3.0402-3.20040.2841440.2215262198
3.2004-3.40090.26831280.2236265899
3.4009-3.66340.25661370.22562692100
3.6634-4.03180.26011400.18462710100
4.0318-4.61480.20461360.16282695100
4.6148-5.81250.23581460.18252753100
5.8125-46.96150.21821730.1789283299

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