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- PDB-6ovt: Crystal Structure of IlvD from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 6ovt
TitleCrystal Structure of IlvD from Mycobacterium tuberculosis
ComponentsDihydroxy-acid dehydratase
KeywordsLYASE / Dihydroxy-acid dehydratase 2 / 3-dihydroxy-3-methylbutanoate 3-methyl-2-oxobutanoate
Function / homology
Function and homology information


dihydroxy-acid dehydratase / dihydroxy-acid dehydratase activity / branched-chain amino acid biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process / 4 iron, 4 sulfur cluster binding / metal ion binding / plasma membrane
Similarity search - Function
Dihydroxy-acid dehydratase / Dihydroxy-acid and 6-phosphogluconate dehydratases signature 2. / Dihydroxy-acid/6-phosphogluconate dehydratase, conserved site / Dihydroxy-acid and 6-phosphogluconate dehydratases signature 1. / Dihydroxy-acid/6-phosphogluconate dehydratase / IlvD/EDD, N-terminal domain / Dihydroxy-acid dehydratase, C-terminal / Dehydratase family
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / DI(HYDROXYETHYL)ETHER / Dihydroxy-acid dehydratase / Dihydroxy-acid dehydratase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.88 Å
AuthorsAlmo, S.C. / Grove, T.L. / Bonanno, J.B. / Baker, E.N. / Bashiri, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI133329 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54-GM093342 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: The active site of theMycobacterium tuberculosisbranched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase contains a 2Fe-2S cluster.
Authors: Bashiri, G. / Grove, T.L. / Hegde, S.S. / Lagautriere, T. / Gerfen, G.J. / Almo, S.C. / Squire, C.J. / Blanchard, J.S. / Baker, E.N.
History
DepositionMay 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: 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.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroxy-acid dehydratase
B: Dihydroxy-acid dehydratase
C: Dihydroxy-acid dehydratase
D: Dihydroxy-acid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,57624
Polymers250,2394
Non-polymers1,33620
Water22,6631258
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22220 Å2
ΔGint-251 kcal/mol
Surface area63130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.406, 88.406, 483.307
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Dihydroxy-acid dehydratase / DAD


Mass: 62559.848 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: ilvD, ilvD_1, DK316_01030, DSI35_17380, ERS027644_00467, ERS027651_01171, ERS027653_01384, ERS027661_02038, ERS124361_01678, SAMEA2682864_00050, SAMEA2683035_00341
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0E8UWV6, UniProt: P9WKJ5*PLUS, dihydroxy-acid dehydratase

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Non-polymers , 5 types, 1278 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: Mg
#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1258 / 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: 2.29 Å3/Da / Density % sol: 46.38 % / Description: ocatognaol
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M MgCl2, 20% polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07822 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07822 Å / Relative weight: 1
ReflectionResolution: 1.88→96.66 Å / Num. obs: 171641 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.033 / Rrim(I) all: 0.111 / Net I/σ(I): 15.3 / Num. measured all: 2009748
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.88-1.9812.10.883302942249950.820.2650.9232.5
5.95-96.6611.90.0436580755170.9990.0130.04545.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDS20161205data reduction
Aimless0.5.32data scaling
SHELXphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.88→80.55 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.324 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1337 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.127
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2011 8430 4.9 %RANDOM
Rwork0.1598 ---
obs0.1618 163010 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 116.52 Å2 / Biso mean: 31.406 Å2 / Biso min: 14.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.1 Å20 Å2
2--0.19 Å20 Å2
3----0.62 Å2
Refinement stepCycle: final / Resolution: 1.88→80.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16173 0 50 1258 17481
Biso mean--41.59 37.18 -
Num. residues----2234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01316658
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715992
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.63222605
X-RAY DIFFRACTIONr_angle_other_deg1.4251.57636930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86952287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.12920.606776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.533152650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.71115145
X-RAY DIFFRACTIONr_chiral_restr0.0760.22211
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219240
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023427
LS refinement shellResolution: 1.883→1.932 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 692 -
Rwork0.239 11923 -
all-12615 -
obs--99.8 %

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