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- PDB-3h5j: LeuD_1-168 small subunit of isopropylmalate isomerase (Rv2987c) f... -

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Basic information

Entry
Database: PDB / ID: 3h5j
TitleLeuD_1-168 small subunit of isopropylmalate isomerase (Rv2987c) from mycobacterium tuberculosis
Components3-isopropylmalate dehydratase small subunit
KeywordsLYASE / Leucine biosynthesis / isopropylmalate isomerase / LeuD / M.tuberculosis / Amino-acid biosynthesis / Branched-chain amino acid biosynthesis
Function / homology
Function and homology information


3-isopropylmalate dehydratase complex / 3-isopropylmalate dehydratase / 3-isopropylmalate dehydratase activity / L-leucine biosynthetic process / plasma membrane
Similarity search - Function
3-isopropylmalate dehydratase, small subunit / 3-isopropylmalate dehydratase, swivel domain / : / Aconitase; domain 4 / Aconitase, domain 4 / Aconitase A/isopropylmalate dehydratase small subunit, swivel domain / Aconitase C-terminal domain / Aconitase/3-isopropylmalate dehydratase, swivel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
3-isopropylmalate dehydratase small subunit / 3-isopropylmalate dehydratase small subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsManikandan, K. / Geerlof, A. / Weiss, M.S.
Citation
Journal: Proteins / Year: 2011
Title: Structural studies on the enzyme complex isopropylmalate isomerase (LeuCD) from Mycobacterium tuberculosis
Authors: Manikandan, K. / Geerlof, A. / Zozulya, A.V. / Svergun, D.I. / Weiss, M.S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the small subunit of isopropylmalate isomerase (Rv2987c) from Mycobacterium tuberculosis
Authors: Manikandan, K. / Geerlof, A. / Schuldt, L. / Mueller-Dieckmann, C. / Weiss, M.S.
History
DepositionApr 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _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: 3-isopropylmalate dehydratase small subunit
B: 3-isopropylmalate dehydratase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,81910
Polymers37,2882
Non-polymers5318
Water7,440413
1
A: 3-isopropylmalate dehydratase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8925
Polymers18,6441
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3-isopropylmalate dehydratase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9265
Polymers18,6441
Non-polymers2824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.070, 75.710, 48.840
Angle α, β, γ (deg.)90.00, 103.22, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAS THE STRUCTURE REPRESENTS ONLY A PART OF A SUBUNIT OF AN ENZYME COMPLEX, THE ASSEMBLIES DESCRIBED IN REMARK350 IS NOT RELEVANT TO THE REAL BIOLOGICAL ASSEMBLIES

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Components

#1: Protein 3-isopropylmalate dehydratase small subunit / Isopropylmalate isomerase small subunit / Alpha-IPM isomerase / IPMI


Mass: 18644.068 Da / Num. of mol.: 2 / Fragment: LeuD, residues 1-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2987c / Plasmid: pETM11 / Production host: Escherichia coli (E. coli)
References: UniProt: P65277, UniProt: P9WK95*PLUS, 3-isopropylmalate dehydratase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SER 1A WAS INTRODUCED WHILE CLONING.

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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: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.2M lithium sulfate, 0.1M Tris-HCl pH 8.5, 20%(w/v) PEG 3350, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 22, 2008
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→99 Å / Num. all: 90248 / Num. obs: 90248 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.7
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 3.8 / % possible all: 91.9

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Processing

Software
NameClassification
MAR345dtbdata collection
MOLREPphasing
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H5E

3h5e


Resolution: 1.2→13.42 Å / Num. parameters: 28335 / Num. restraintsaints: 35073 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.175 1855 -random
obs0.1298 88352 97.5 %-
all-88352 --
Refine analyzeNum. disordered residues: 24 / Occupancy sum hydrogen: 2546.15 / Occupancy sum non hydrogen: 3024.55
Refinement stepCycle: LAST / Resolution: 1.2→13.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 33 413 3041
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0.008
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.095
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.035
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0.094

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