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- PDB-4om8: Crystal structure of 5-formly-3-hydroxy-2-methylpyridine 4-carbox... -

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Basic information

Entry
Database: PDB / ID: 4om8
TitleCrystal structure of 5-formly-3-hydroxy-2-methylpyridine 4-carboxylic acid (FHMPC) 5-dehydrogenase, an NAD+ dependent dismutase.
Components3-hydroxybutyryl-coA dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / Dismutase / Structural Genomics / Enzyme Function Initiative / Rossmann fold / NAD-Binding
Function / homology
Function and homology information


5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase / L-gulonate 3-dehydrogenase activity / vitamin B6 catabolic process / NAD+ binding / fatty acid metabolic process
Similarity search - Function
: / 3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain ...: / 3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / BETA-MERCAPTOETHANOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylate 5-dehydrogenase
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMugo, A.N. / Kobayashi, J. / Mikami, B. / Yagi, T. / Ohnishi, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an NAD(+)-dependent dismutase from Mesorhizobium loti
Authors: Mugo, A.N. / Kobayashi, J. / Mikami, B. / Yoshikane, Y. / Yagi, T. / Ohnishi, K.
History
DepositionJan 27, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Feb 18, 2015Group: Other
Revision 1.3Nov 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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: 3-hydroxybutyryl-coA dehydrogenase
B: 3-hydroxybutyryl-coA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,94310
Polymers66,1912
Non-polymers1,7528
Water12,214678
1
A: 3-hydroxybutyryl-coA dehydrogenase
hetero molecules

A: 3-hydroxybutyryl-coA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,91010
Polymers66,1912
Non-polymers1,7198
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area10440 Å2
ΔGint-85 kcal/mol
Surface area24030 Å2
MethodPISA
2
B: 3-hydroxybutyryl-coA dehydrogenase
hetero molecules

B: 3-hydroxybutyryl-coA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,97610
Polymers66,1912
Non-polymers1,7858
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10360 Å2
ΔGint-87 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.805, 44.212, 109.343
Angle α, β, γ (deg.)90.00, 116.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-644-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 3-hydroxybutyryl-coA dehydrogenase


Mass: 33095.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: Mesorhizobium loti: mlr6793, mlr6793 / Production host: Escherichia coli (E. coli) / References: UniProt: Q988C8

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Non-polymers , 5 types, 686 molecules

#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 678 / 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: 2.01 Å3/Da / Density % sol: 38.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2M NH4-acetate, 0.1M Na-acetate pH 5.0, 30% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å
DetectorType: Saturn A200 / Detector: CCD / Date: Dec 14, 2013
RadiationMonochromator: Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 75976 / % possible obs: 96.5 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.495→1.534 Å / Redundancy: 1.6 % / Num. unique all: 10794 / % possible all: 87.43

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FIM

1fim


Resolution: 1.55→27.336 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.311 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / ESU R: 0.077 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1878 3821 5.03 %RANDOM
Rwork0.1551 ---
obs0.1567 75969 98.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: MASK
Displacement parametersBiso max: 70.16 Å2 / Biso mean: 15.1 Å2 / Biso min: 6.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0.08 Å2-0.1 Å2
2--0.1 Å20.53 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.55→27.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4634 0 114 678 5426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075084
X-RAY DIFFRACTIONf_angle_d1.1736953
X-RAY DIFFRACTIONf_dihedral_angle_d15.41983
X-RAY DIFFRACTIONf_chiral_restr0.046826
X-RAY DIFFRACTIONf_plane_restr0.006887
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.55-1.56970.23741300.1784253495
1.5697-1.59040.22671550.1804263698
1.5904-1.61210.24241130.1841260997
1.6121-1.63520.22831390.1799266198
1.6352-1.65960.20441470.1805257498
1.6596-1.68550.22021380.1774262698
1.6855-1.71310.24471360.1694265698
1.7131-1.74270.24051320.174261598
1.7427-1.77440.20521370.1672267798
1.7744-1.80850.21131370.1621266999
1.8085-1.84540.20911590.164259999
1.8454-1.88550.20631460.1645264799
1.8855-1.92940.20121350.1612269999
1.9294-1.97760.17441450.16552673100
1.9776-2.0310.19521490.16122653100
2.031-2.09080.19311480.15482691100
2.0908-2.15820.1981610.15712678100
2.1582-2.23530.18991360.15392689100
2.2353-2.32480.1861490.15632729100
2.3248-2.43050.18281420.15412676100
2.4305-2.55860.1851450.15562697100
2.5586-2.71880.20151230.16362715100
2.7188-2.92850.23711320.16272739100
2.9285-3.22280.19141480.1642703100
3.2228-3.68810.15181420.14272742100
3.6881-4.64290.14731270.12852765100
4.6429-27.340.1591700.1372279699

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