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- PDB-3hps: Crystal structure of Mycobacterium tuberculosis LeuA complexed wi... -

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Basic information

Entry
Database: PDB / ID: 3hps
TitleCrystal structure of Mycobacterium tuberculosis LeuA complexed with ketoisocaproate (KIC)
Components2-isopropylmalate synthase
KeywordsTRANSFERASE / 2-isopropylmalate synthase / LeuA / Mycobacterium tuberculosis / leucine biosynthesis / enzyme / TIM barrel / regulatory domain / substrate / Amino-acid biosynthesis / Branched-chain amino acid biosynthesis
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 / 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 / Alpha-isopropylmalate synthase, post-catalytic domain-like / 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain / 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain superfamily / LeuA allosteric (dimerisation) domain / LeuA allosteric (dimerisation) domain ...Arc Repressor Mutant - #20 / Alpha-isopropylmalate synthase LeuA, regulatory domain / Helix Hairpins - #1400 / 2-isopropylmalate synthase / LeuA, N-terminal catalytic TIM barrel domain / Alpha-isopropylmalate synthase, post-catalytic domain-like / 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
2-OXO-4-METHYLPENTANOIC ACID / LEUCINE / 2-isopropylmalate synthase / 2-isopropylmalate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKoon, N. / Squire, C.J. / Baker, E.N.
CitationJournal: To be Published
Title: Probing the active site of M. tuberculosis LeuA
Authors: Koon, N. / Squire, C.J. / Baker, E.N.
History
DepositionJun 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jun 5, 2013Group: Non-polymer description
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)141,21210
Polymers140,3752
Non-polymers8388
Water18,9341051
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15730 Å2
ΔGint-50.2 kcal/mol
Surface area40180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.411, 154.848, 68.882
Angle α, β, γ (deg.)90.00, 97.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 70187.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: leuA, MT3813, MTV025.058, Rv3710 / Plasmid: pPROEXHTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P96420, UniProt: P9WQB3*PLUS, 2-isopropylmalate synthase

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Non-polymers , 5 types, 1059 molecules

#2: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-COI / 2-OXO-4-METHYLPENTANOIC ACID / alpha-ketoisocaproic acid


Mass: 130.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1051 / 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: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: Sodium citrate, PEG MME 2000, pH 6.25, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5417 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 25, 2004 / Details: Osmic
RadiationMonochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 89717 / Num. obs: 89717 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.85 Å / % possible all: 49

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Processing

Software
NameClassification
MAR345dtbdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SR9

1sr9


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.582 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20476 4754 5 %RANDOM
Rwork0.15761 ---
all0.15998 89717 --
obs0.15998 89717 90.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.415 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20.24 Å2
2---0.55 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8720 0 50 1051 9821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0229008
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.95312308
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89851163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7423.723411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.012151330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6691574
X-RAY DIFFRACTIONr_chiral_restr0.1210.21393
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217036
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8321.55787
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48829307
X-RAY DIFFRACTIONr_scbond_it2.5633221
X-RAY DIFFRACTIONr_scangle_it4.1624.52991
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 188 -
Rwork0.265 3575 -
obs--48.95 %

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