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- PDB-1w0d: The high resolution structure of Mycobacterium tuberculosis LeuB ... -

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Basic information

Entry
Database: PDB / ID: 1w0d
TitleThe high resolution structure of Mycobacterium tuberculosis LeuB (Rv2995c)
Components3-ISOPROPYLMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / LEUCINE BIOSYNTHESIS / NAD / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / TB STRUCTURAL GENOMICS CONSORTIUM / TB / TBSGC
Function / homology
Function and homology information


3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion binding / cytoplasm
Similarity search - Function
3-isopropylmalate dehydrogenase, actinobacteria / : / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSingh, R.K. / Kefala, G. / Janowski, R. / Mueller-Dieckmann, C. / Weiss, M.S. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The High Resolution Structure of Leub (Rv2995C) from Mycobacterium Tuberculosis
Authors: Singh, R.K. / Kefala, G. / Janowski, R. / Mueller-Dieckmann, C. / Von Kries, J.P. / Weiss, M.S.
History
DepositionJun 3, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 24, 2017Group: Structure summary
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 21, 2019Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-ISOPROPYLMALATE DEHYDROGENASE
B: 3-ISOPROPYLMALATE DEHYDROGENASE
C: 3-ISOPROPYLMALATE DEHYDROGENASE
D: 3-ISOPROPYLMALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,8365
Polymers141,7404
Non-polymers961
Water10,431579
1
A: 3-ISOPROPYLMALATE DEHYDROGENASE
B: 3-ISOPROPYLMALATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)70,8702
Polymers70,8702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: 3-ISOPROPYLMALATE DEHYDROGENASE
D: 3-ISOPROPYLMALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9663
Polymers70,8702
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.470, 97.060, 181.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
3-ISOPROPYLMALATE DEHYDROGENASE / BETA-IPM DEHYDROGENASE / IMDH / 3-IPM-DH


Mass: 35435.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: ROSSMAN FOLD / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P95313, UniProt: P9WKK9*PLUS, 3-isopropylmalate dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE SER 1A IS A CLONING ARTEFACT. IT HAD TO BE INSERTED BETWEEN RESIDUES MET 1 AND RESIDUES LYS ...RESIDUE SER 1A IS A CLONING ARTEFACT. IT HAD TO BE INSERTED BETWEEN RESIDUES MET 1 AND RESIDUES LYS 2 TO ENSURE THE CORRECT READING FRAME. RESIDUE MET 1 CORRESPONDS TO MET 1 OF THE ACCOMPANYING UNIPROT SEQUENCE ENTRY.

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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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growpH: 8 / Details: pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.65→99 Å / Num. obs: 167255 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.6
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.2 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.437 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3127 2 %RANDOM
Rwork0.213 ---
obs0.213 152424 93.1 %-
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: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--1.36 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9972 0 5 579 10556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02110205
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.95613902
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86651344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1130.21644
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027819
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.26026
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2898
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.295
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0461.56676
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8222.510708
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.92553529
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.91103194
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.312 228
Rwork0.261 11592
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)
10.68010.034-0.70730.4325-0.06662.03960.0594-0.03530.00450.0276-0.02680.14790.0258-0.1745-0.03260.12180.00260.00870.0385-0.00250.10488.177153.23014.9504
20.807-0.29020.06090.7908-0.42351.2902-0.0284-0.20560.01410.20440.0101-0.2743-0.09760.36030.01830.16150.0206-0.0630.172-0.02250.176339.930543.85980.8626
30.50070.0092-0.03531.0312-0.64091.3664-0.03330.04020.18990.02890.0332-0.0704-0.21120.17130.00010.0182-0.0214-0.00070.06330.02710.117719.104462.967847.769
40.49440.0019-0.09281.28640.73281.2707-0.00950.1386-0.16490.0130.02040.00340.1499-0.0913-0.01090.00220.0015-0.01530.0534-0.02790.113420.193629.995750.4871
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 336
2X-RAY DIFFRACTION2B1 - 336
3X-RAY DIFFRACTION3C1 - 336
4X-RAY DIFFRACTION4D1 - 336

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