[English] 日本語
Yorodumi
- PDB-5y8n: Mycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (Mt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5y8n
TitleMycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (MtHIBADH) + NAD + L-serine
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 / L-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
(2~{S})-2-methylpentanedioic acid / ACRYLIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SERINE / Probable 3-hydroxyisobutyrate dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.68 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable 3-hydroxyisobutyrate dehydrogenase
B: Probable 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,79112
Polymers59,6742
Non-polymers2,11710
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-60 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.160, 129.160, 70.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

-
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

-
Non-polymers , 6 types, 295 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-AKR / ACRYLIC ACID


Mass: 72.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O2
#6: Chemical ChemComp-9ON / (2~{S})-2-methylpentanedioic acid


Mass: 146.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.36 %
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

-
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 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.68→111.86 Å / Num. obs: 18305 / % possible obs: 96.4 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 7
Reflection shellResolution: 2.68→2.82 Å / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 7 / Num. unique obs: 18305 / % possible all: 96.4

-
Processing

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

3obb


Resolution: 2.68→111.86 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.873 / SU B: 12.346 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 937 5.1 %RANDOM
Rwork0.18123 ---
obs0.18427 17349 96.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.381 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.33 Å2-0 Å2
2---0.66 Å20 Å2
3---2.14 Å2
Refinement stepCycle: 1 / Resolution: 2.68→111.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4076 0 141 285 4502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194304
X-RAY DIFFRACTIONr_bond_other_d0.0020.024078
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.9835886
X-RAY DIFFRACTIONr_angle_other_deg0.9523.0019341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5635581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78324140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25515579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.611519
X-RAY DIFFRACTIONr_chiral_restr0.0730.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214954
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02929
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_it1.1472.1832340
X-RAY DIFFRACTIONr_mcbond_other1.1352.1792337
X-RAY DIFFRACTIONr_mcangle_it1.8953.2532915
X-RAY DIFFRACTIONr_mcangle_other1.893.2532915
X-RAY DIFFRACTIONr_scbond_it1.4742.3871964
X-RAY DIFFRACTIONr_scbond_other1.4742.3891965
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4463.5082972
X-RAY DIFFRACTIONr_long_range_B_refined6.47442.18520442
X-RAY DIFFRACTIONr_long_range_B_other6.45442.21820359
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.68→2.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 75 -
Rwork0.281 1205 -
obs--92.55 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more