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- PDB-5y8p: Mycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (Mt... -

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Basic information

Entry
Database: PDB / ID: 5y8p
TitleMycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (MtHIBADH) + 3-Hydroxy propionate (3-HP)
ComponentsProbable 3-hydroxyisobutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / 3-Hydroxy acid Dehydrogenase / Enzyme substrate interactions / Mechanism of enzyme action
Function / homology
Function and homology information


3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase activity / valine catabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding
Similarity search - Function
3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 ...3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 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
3-HYDROXY-PROPANOIC ACID / (2~{S})-2-methylpentanedioic acid / ACRYLIC ACID / Probable 3-hydroxyisobutyrate dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSrikalaivani, R. / Singh, A. / Surolia, A. / Vijayan, M.
CitationJournal: Biochem. J. / Year: 2018
Title: Structure, interactions and action ofMycobacterium tuberculosis3-hydroxyisobutyric acid dehydrogenase.
Authors: Srikalaivani, R. / Singh, A. / Vijayan, M. / Surolia, A.
History
DepositionAug 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Probable 3-hydroxyisobutyrate dehydrogenase
B: Probable 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4059
Polymers59,6742
Non-polymers7317
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-44 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.920, 128.920, 70.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable 3-hydroxyisobutyrate dehydrogenase / HIBADH


Mass: 29837.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: mmsB, Rv0751c, MTV041.25c / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P9WNY5, 3-hydroxyisobutyrate dehydrogenase

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Non-polymers , 5 types, 480 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-9ON / (2~{S})-2-methylpentanedioic acid


Mass: 146.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O4
#4: Chemical ChemComp-3OH / 3-HYDROXY-PROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#5: Chemical ChemComp-AKR / ACRYLIC ACID


Mass: 72.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.5
Details: 0.02M MgCl2.6H2O, 0.1M HEPES pH 7.5, 22% w/v polyacrylic acid sodium salt 5100

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→111.65 Å / Num. obs: 33570 / % possible obs: 92.5 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.4
Reflection shellResolution: 2.15→2.27 Å / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 7.4 / Num. unique obs: 33570 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OBB

3obb


Resolution: 2.15→111.65 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.586 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 1679 5 %RANDOM
Rwork0.16688 ---
obs0.16936 31857 92.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.377 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å2-0 Å2
3----0.72 Å2
Refinement stepCycle: 1 / Resolution: 2.15→111.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4093 0 49 473 4615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194268
X-RAY DIFFRACTIONr_bond_other_d0.0030.024089
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9585823
X-RAY DIFFRACTIONr_angle_other_deg1.0833.0019382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3645589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.1824.041146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24815594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7451520
X-RAY DIFFRACTIONr_chiral_restr0.1110.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214980
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02913
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_it1.2711.7572353
X-RAY DIFFRACTIONr_mcbond_other1.271.7542350
X-RAY DIFFRACTIONr_mcangle_it2.0442.6232944
X-RAY DIFFRACTIONr_mcangle_other2.0452.6242944
X-RAY DIFFRACTIONr_scbond_it1.9932.0411915
X-RAY DIFFRACTIONr_scbond_other1.9882.0381913
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.112.9472879
X-RAY DIFFRACTIONr_long_range_B_refined5.72124.0755178
X-RAY DIFFRACTIONr_long_range_B_other5.59223.8235092
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 96 -
Rwork0.252 2098 -
obs--82.39 %

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