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- PDB-1sr9: Crystal Structure of LeuA from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 1sr9
TitleCrystal Structure of LeuA from Mycobacterium tuberculosis
Components2-isopropylmalate synthase
KeywordsTRANSFERASE / TIM barrel
Function / homology
Function and homology information


2-isopropylmalate synthase / 2-isopropylmalate synthase activity / acetyl-CoA C-acetyltransferase activity / L-leucine biosynthetic process / potassium ion binding / amino acid biosynthetic process / manganese ion binding / magnesium ion binding / zinc ion binding / extracellular region ...2-isopropylmalate synthase / 2-isopropylmalate synthase activity / acetyl-CoA C-acetyltransferase activity / L-leucine biosynthetic process / potassium ion binding / amino acid biosynthetic process / manganese ion binding / magnesium ion binding / zinc ion binding / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Arc Repressor Mutant - #20 / Alpha-isopropylmalate synthase LeuA, regulatory domain / Helix Hairpins - #1400 / 2-isopropylmalate synthase / LeuA, N-terminal catalytic TIM barrel domain / 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain / 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain superfamily / LeuA allosteric (dimerisation) domain / LeuA allosteric (dimerisation) domain / Alpha-isopropylmalate and homocitrate synthases signature 2. ...Arc Repressor Mutant - #20 / Alpha-isopropylmalate synthase LeuA, regulatory domain / Helix Hairpins - #1400 / 2-isopropylmalate synthase / LeuA, N-terminal catalytic TIM barrel domain / 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain / 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain superfamily / LeuA allosteric (dimerisation) domain / LeuA allosteric (dimerisation) domain / Alpha-isopropylmalate and homocitrate synthases signature 2. / Alpha-isopropylmalate and homocitrate synthases signature 1. / Alpha-isopropylmalate/homocitrate synthase, conserved site / Arc Repressor Mutant / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Double Stranded RNA Binding Domain / Aldolase class I / Helix Hairpins / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-METHYL-2-OXOBUTANOIC ACID / 2-isopropylmalate synthase / 2-isopropylmalate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2 Å
AuthorsKoon, N. / Squire, C.J. / Baker, E.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Crystal structure of LeuA from Mycobacterium tuberculosis, a key enzyme in leucine biosynthesis
Authors: Koon, N. / Squire, C.J. / Baker, E.N.
History
DepositionMar 22, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-isopropylmalate synthase
B: 2-isopropylmalate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,8997
Polymers141,5002
Non-polymers3995
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16390 Å2
ΔGint-135 kcal/mol
Surface area40170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.25, 154.73, 68.82
Angle α, β, γ (deg.)90, 98.05, 90
Int Tables number4
Space group name H-MP1211
Detailsthe biological assembly consists of chain A chain B homodimer

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Components

#1: Protein 2-isopropylmalate synthase / Alpha-isopropylmalate synthase / LeuA / Alpha-IPM synthetase


Mass: 70750.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P96420, UniProt: P9WQB3*PLUS, 2-isopropylmalate synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-KIV / 3-METHYL-2-OXOBUTANOIC ACID / ALPHA-KETOISOVALERIC ACID / KETOVALINE


Mass: 116.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.02 Å3/Da / Density % sol: 39.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: sodium citrate, MPEG2000, pH 6.25, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 8, 2003
RadiationMonochromator: Osmic / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→80 Å / Num. all: 74305 / Num. obs: 74305 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.97 Å / % possible all: 94.9

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 2→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.197 3740 Random
Rwork0.169 --
all0.17 70628 -
obs0.17 70628 -
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8668 0 19 466 9153
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.016
X-RAY DIFFRACTIONr_angle_refined_deg1.47

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