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- PDB-3hpx: Crystal structure of Mycobacterium tuberculosis LeuA active site ... -

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Basic information

Entry
Database: PDB / ID: 3hpx
TitleCrystal structure of Mycobacterium tuberculosis LeuA active site domain 1-425 (truncation mutant delta:426-644)
Components2-isopropylmalate synthase
KeywordsTRANSFERASE / 2-isopropylmalate synthase / LeuA / Mycobacterium tuberculosis / truncation mutant / active site domain / TIM barrel / Amino-acid biosynthesis / Branched-chain amino acid biosynthesis / Leucine 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 / extracellular region / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
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. ...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 / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Aldolase class I / Helix Hairpins / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / 2-isopropylmalate synthase / 2-isopropylmalate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsKoon, N. / Squire, C.J. / Baker, E.N.
CitationJournal: Biochemistry / Year: 2012
Title: Removal of the C-terminal regulatory domain of alpha-isopropylmalate synthase disrupts functional substrate binding
Authors: Huisman, F.H. / Koon, N. / Bulloch, E.M. / Baker, H.M. / Baker, E.N. / Squire, C.J. / Parker, E.J.
History
DepositionJun 5, 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 1.2Mar 14, 2012Group: Database references
Revision 1.3Jun 19, 2013Group: Database references
Revision 1.4Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,3766
Polymers95,0752
Non-polymers3024
Water11,403633
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-40.3 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.025, 70.886, 70.043
Angle α, β, γ (deg.)62.45, 81.41, 70.26
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 47537.293 Da / Num. of mol.: 2 / Fragment: Active site domain: UNP residues 1-425 / Mutation: Truncation mutant delta:426-644
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
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 633 / 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: 2.09 Å3/Da / Density % sol: 41.23 %
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: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 10, 2005 / Details: Osmic
RadiationMonochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→30 Å / Num. all: 47066 / Num. obs: 47066 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 17.7
Reflection shellResolution: 2.03→2.1 Å / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4222 / % possible all: 84.7

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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: 2.03→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.562 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23794 2396 5.1 %RANDOM
Rwork0.17381 ---
all0.17716 44670 --
obs0.17716 44670 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.097 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.09 Å20.13 Å2
2---0.59 Å2-0.75 Å2
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.03→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6285 0 14 633 6932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226445
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9558794
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6635813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07623.718312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33715969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7261558
X-RAY DIFFRACTIONr_chiral_restr0.1160.2964
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025088
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.23475
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24397
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2707
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9171.54214
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3926586
X-RAY DIFFRACTIONr_scbond_it2.47932560
X-RAY DIFFRACTIONr_scangle_it3.7394.52208
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 155 -
Rwork0.259 2934 -
obs--82.68 %

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