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- PDB-5hxi: 2-Methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5HN bound -

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Basic information

Entry
Database: PDB / ID: 5hxi
Title2-Methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5HN bound
Components2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
KeywordsOXIDOREDUCTASE / alpha/beta fold / flavoenzyme / substrate complex
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 / DI(HYDROXYETHYL)ETHER / 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
Similarity search - Component
Biological speciesRhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKobayashi, J. / Mikami, B.
CitationJournal: J. Biosci. Bioeng. / Year: 2017
Title: Role of the Tyr270 residue in 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase from Mesorhizobium loti
Authors: Kobayashi, J. / Yoshida, H. / Yagi, T. / Kamitori, S. / Hayashi, H. / Mizutani, K. / Takahashi, N. / Mikami, B.
History
DepositionJan 30, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 20, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,32211
Polymers41,7981
Non-polymers1,52310
Water8,575476
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)173,28744
Polymers167,1944
Non-polymers6,09340
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area7190 Å2
ΔGint-31 kcal/mol
Surface area54190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.338, 131.140, 132.282
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-811-

HOH

21A-815-

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.) Rhizobium loti (strain MAFF303099) (bacteria)
Strain: MAFF303099 / Gene: mlr6788 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q988D3

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Non-polymers , 7 types, 486 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-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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 476 / 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: 51.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 8% PEG8000, 0.1M Tris-HCl pH 8.5

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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: 1.5→93.13 Å / Num. all: 68494 / Num. obs: 68494 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.379 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.097 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17402 3468 5.1 %RANDOM
Rwork0.15091 ---
obs0.15207 65011 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.594 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å2-0 Å2
2---0.48 Å20 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 100 476 3442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193175
X-RAY DIFFRACTIONr_bond_other_d0.0020.022999
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.9814339
X-RAY DIFFRACTIONr_angle_other_deg0.85436908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8635414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86823.214140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.86415516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9481528
X-RAY DIFFRACTIONr_chiral_restr0.0670.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213606
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02740
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.461.2031530
X-RAY DIFFRACTIONr_mcbond_other0.4591.2031529
X-RAY DIFFRACTIONr_mcangle_it0.5591.8061926
X-RAY DIFFRACTIONr_mcangle_other0.5591.8061927
X-RAY DIFFRACTIONr_scbond_it0.5091.3251645
X-RAY DIFFRACTIONr_scbond_other0.5091.3251645
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6071.9332394
X-RAY DIFFRACTIONr_long_range_B_refined1.47111.3094162
X-RAY DIFFRACTIONr_long_range_B_other1.47111.3114163
X-RAY DIFFRACTIONr_rigid_bond_restr0.42536173
X-RAY DIFFRACTIONr_sphericity_free18.165113
X-RAY DIFFRACTIONr_sphericity_bonded4.07156456
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 247 -
Rwork0.176 4624 -
obs--96.88 %

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