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- PDB-5y8o: Mycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (Mt... -

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Basic information

Entry
Database: PDB / ID: 5y8o
TitleMycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (MtHIBADH) + NAD + 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Probable 3-hydroxyisobutyrate dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 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

Downloads & links

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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)60,9769
Polymers59,6742
Non-polymers1,3027
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-50 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.060, 129.060, 70.130
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 , 6 types, 525 molecules

#2: Chemical ChemComp-AKR / ACRYLIC ACID / Acrylic acid


Mass: 72.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 146.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O4
#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#6: Chemical ChemComp-3OH / 3-HYDROXY-PROPANOIC ACID / 3-Hydroxypropionic acid


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 295 K / Method: microbatch
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: Aug 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→111.77 Å / Num. obs: 41484 / % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 6
Reflection shellResolution: 2.05→2.16 Å / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 6 / Num. unique obs: 41484 / % possible all: 99

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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: 2.05→111.77 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.763 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22508 2095 5.1 %RANDOM
Rwork0.1757 ---
obs0.17819 39313 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.308 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.05 Å20 Å2
2--0.11 Å2-0 Å2
3----0.34 Å2
Refinement stepCycle: 1 / Resolution: 2.05→111.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4097 0 87 518 4702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194302
X-RAY DIFFRACTIONr_bond_other_d0.0020.024111
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9725878
X-RAY DIFFRACTIONr_angle_other_deg1.0193.0019431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.45224145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95715597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5661520
X-RAY DIFFRACTIONr_chiral_restr0.0920.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214984
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02922
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_it1.5172.0882344
X-RAY DIFFRACTIONr_mcbond_other1.4792.0862343
X-RAY DIFFRACTIONr_mcangle_it2.333.1182932
X-RAY DIFFRACTIONr_mcangle_other2.3313.122933
X-RAY DIFFRACTIONr_scbond_it2.5012.4771958
X-RAY DIFFRACTIONr_scbond_other2.4992.4741956
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9173.5792946
X-RAY DIFFRACTIONr_long_range_B_refined7.59643.85422919
X-RAY DIFFRACTIONr_long_range_B_other7.53943.75222759
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 155 -
Rwork0.307 2867 -
obs--99.31 %

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