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- PDB-3h5e: LeuD_1-156 small subunit of isopropylmalate isomerase (Rv2987c) f... -

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Basic information

Entry
Database: PDB / ID: 3h5e
TitleLeuD_1-156 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 / SIRAS / Resolution: 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: Advisory / Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)34,4972
Polymers34,4972
Non-polymers00
Water2,432135
1
A: 3-isopropylmalate dehydratase small subunit


Theoretical massNumber of molelcules
Total (without water)17,2491
Polymers17,2491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3-isopropylmalate dehydratase small subunit


Theoretical massNumber of molelcules
Total (without water)17,2491
Polymers17,2491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.620, 64.620, 419.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
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: 17248.543 Da / Num. of mol.: 2 / Fragment: LeuD, residues 1-156
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SER 1A WAS INTRODUCED WHILE CLONING. ILE 122 OCCURRED DURING PCR.

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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: 3.67 Å3/Da / Density % sol: 66.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 1M sodium citrate tribasic, 0.1M sodium cacodylate pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0724 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2008
RadiationMonochromator: crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0724 Å / Relative weight: 1
ReflectionResolution: 2→70 Å / Num. all: 36296 / Num. obs: 36296 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 52.7 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 21.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.2 / % possible all: 92.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.4.0069refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.633 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26852 1132 3.1 %RANDOM
Rwork0.23407 ---
obs0.2351 35075 98.42 %-
all-36807 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.138 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20.79 Å20 Å2
2--1.58 Å20 Å2
3----2.36 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 0 135 2494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222432
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9473309
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5875312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88422.589112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77915379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4831524
X-RAY DIFFRACTIONr_chiral_restr0.1120.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211880
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_it0.8661.51522
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6072.52448
X-RAY DIFFRACTIONr_scbond_it3.7685910
X-RAY DIFFRACTIONr_scangle_it5.9110857
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 82 -
Rwork0.275 2344 -
obs--93.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.28891.406-1.83552.2082-1.15414.67090.1368-0.06450.1426-0.29440.0812-0.1924-0.4924-0.1103-0.2180.0587-0.07270.0849-0.2806-0.0303-0.117713.738448.211724.6643
21.63960.29381.54754.89413.03415.38190.25990.2928-0.2434-0.53560.0118-0.1419-0.23580.1917-0.2717-0.017-0.04220.0026-0.2186-0.0413-0.079434.789472.72838.0736
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 156
2X-RAY DIFFRACTION2B1 - 155

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