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- PDB-3h5h: LeuD_1-186 small subunit of isopropylmalate isomerase (Rv2987c) f... -

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Basic information

Entry
Database: PDB / ID: 3h5h
TitleLeuD_1-186 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: 2.5 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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)41,2652
Polymers41,2652
Non-polymers00
Water70339
1
A: 3-isopropylmalate dehydratase small subunit


Theoretical massNumber of molelcules
Total (without water)20,6321
Polymers20,6321
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)20,6321
Polymers20,6321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.480, 70.290, 59.650
Angle α, β, γ (deg.)90.00, 124.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-187-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISPHEPHEAA5 - 298 - 32
21HISHISPHEPHEBB5 - 298 - 32
12ARGARGLEULEUAA35 - 16738 - 170
22ARGARGLEULEUBB35 - 16738 - 170
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: 20632.318 Da / Num. of mol.: 2 / Fragment: LeuD, residues 1-186
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 / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1.9 Å3/Da / Density % sol: 35.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.1M NaCl, 0.1M Hepes pH 7.0, 1.2M Ammonium sulphate, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2008
RadiationMonochromator: Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.5→51 Å / Num. all: 10727 / Num. obs: 10727 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.171 / Net I/σ(I): 7.6
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.2 / % possible all: 92.3

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.4.0069refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H5E

3h5e


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.843 / SU B: 13.29 / SU ML: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26863 518 4.8 %RANDOM
Rwork0.2257 ---
obs0.22788 10185 99.04 %-
all-10727 --
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: 19 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-1.22 Å2
2---1.04 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 0 39 2632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222647
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0741.9443597
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0765333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.41122.951122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.9515411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3081523
X-RAY DIFFRACTIONr_chiral_restr0.070.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212037
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_it0.5531.51655
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1032.52651
X-RAY DIFFRACTIONr_scbond_it2.3985992
X-RAY DIFFRACTIONr_scangle_it4.05910946
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A632tight positional0.050.05
2B587medium positional0.040.5
1A632tight thermal0.251.5
2B587medium thermal0.412.5
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 29 -
Rwork0.241 708 -
obs--93.77 %

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