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- PDB-4h2q: structure of MHPCO-5HN complex -

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Basic information

Entry
Database: PDB / ID: 4h2q
Titlestructure of MHPCO-5HN 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


monooxygenase activity / FAD binding
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: 1.502 Å
AuthorsKobayashi, J. / Yoshida, H. / Mikami, B. / Hayashi, H. / Kamitori, S. / Yagi, T.
CitationJournal: To be Published
Title: Crystal structure of 2-Methyl-3-hydroxypyridiine-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 1.1Apr 2, 2014Group: Structure summary
Revision 1.2Nov 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1848
Polymers41,7981
Non-polymers1,3857
Water8,269459
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)172,73532
Polymers167,1944
Non-polymers5,54128
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
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-657-

HOH

21A-944-

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 (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 , 6 types, 466 molecules

#2: Chemical ChemComp-FAD / 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


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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 459 / 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: 51.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 8% PEG 8000, 0.1M Tris-HCl, 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: 1.48→50 Å / Num. obs: 71338 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 12.08 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.4
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 5.9 / Num. unique all: 3525 / % possible all: 100

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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: 1.502→41.795 Å / Occupancy max: 1 / Occupancy min: 0.18 / SU ML: 0.16 / σ(F): 1.33 / Phase error: 17.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1924 3468 5.06 %
Rwork0.166 --
obs0.1674 68479 99.55 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.375 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso max: 74.59 Å2 / Biso mean: 14.6153 Å2 / Biso min: 5.34 Å2
Baniso -1Baniso -2Baniso -3
1-2.8971 Å2-0 Å2-0 Å2
2---1.9814 Å2-0 Å2
3----0.9157 Å2
Refinement stepCycle: LAST / Resolution: 1.502→41.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2875 0 92 459 3426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073205
X-RAY DIFFRACTIONf_angle_d1.4474380
X-RAY DIFFRACTIONf_dihedral_angle_d13.7211221
X-RAY DIFFRACTIONf_chiral_restr0.087471
X-RAY DIFFRACTIONf_plane_restr0.005561
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5019-1.52250.2411260.2169240494
1.5225-1.54420.23341380.20472605100
1.5442-1.56730.26091190.19672569100
1.5673-1.59180.22661260.18712608100
1.5918-1.61790.22281090.17352593100
1.6179-1.64580.20111580.17682588100
1.6458-1.67570.18771410.17212566100
1.6757-1.70790.22981330.17122600100
1.7079-1.74280.21151680.16552542100
1.7428-1.78070.19571450.16392587100
1.7807-1.82210.17481440.16252582100
1.8221-1.86770.18631380.16112588100
1.8677-1.91820.19221300.16542614100
1.9182-1.97460.20731600.16722556100
1.9746-2.03840.18261280.17242595100
2.0384-2.11120.19151140.17242625100
2.1112-2.19570.21711530.172589100
2.1957-2.29570.17051530.16472615100
2.2957-2.41670.18591180.16362640100
2.4167-2.56810.21341430.16822606100
2.5681-2.76630.18881640.16672626100
2.7663-3.04460.1951400.17022626100
3.0446-3.4850.19121390.16082661100
3.485-4.390.16091280.14612706100
4.39-41.81090.17811530.1608272097

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