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- PDB-4jn6: Crystal Structure of the Aldolase-Dehydrogenase Complex from Myco... -

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Basic information

Entry
Database: PDB / ID: 4jn6
TitleCrystal Structure of the Aldolase-Dehydrogenase Complex from Mycobacterium tuberculosis HRv37
Components
  • 4-hydroxy-2-oxovalerate aldolase
  • Acetaldehyde dehydrogenase
KeywordsLYASE/OXIDOREDUCTASE / Rossmann fold / TIM Barrel / Aldolase-Dehydrogenase / LYASE-OXIDOREDUCTASE complex
Function / homology
Function and homology information


propanal dehydrogenase (CoA-propanoylating) / 4-hydroxy-2-oxohexanoate aldolase / 4-hydroxy-2-oxovalerate aldolase / 4-hydroxy-2-oxovalerate aldolase activity / 2-isopropylmalate synthase activity / acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / L-leucine biosynthetic process / cell wall / : ...propanal dehydrogenase (CoA-propanoylating) / 4-hydroxy-2-oxohexanoate aldolase / 4-hydroxy-2-oxovalerate aldolase / 4-hydroxy-2-oxovalerate aldolase activity / 2-isopropylmalate synthase activity / acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / L-leucine biosynthetic process / cell wall / : / NAD binding / manganese ion binding / cytosol
Similarity search - Function
DmpG-like communication / 4-hydroxy-2-oxovalerate aldolase / 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain / DmpG-like communication domain / Acetaldehyde dehydrogenase / Acetaldehyde dehydrogenase, C-terminal / Prokaryotic acetaldehyde dehydrogenase, dimerisation / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain ...DmpG-like communication / 4-hydroxy-2-oxovalerate aldolase / 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain / DmpG-like communication domain / Acetaldehyde dehydrogenase / Acetaldehyde dehydrogenase, C-terminal / Prokaryotic acetaldehyde dehydrogenase, dimerisation / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Helicase, Ruva Protein; domain 3 - #60 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / Helicase, Ruva Protein; domain 3 / Aldolase class I / Aldolase-type TIM barrel / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / OXALATE ION / Propanal dehydrogenase (CoA-propanoylating) / 4-hydroxy-2-oxohexanoate aldolase / 4-hydroxy-2-oxohexanoate aldolase / Propanal dehydrogenase (CoA-propanoylating)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsCarere, J. / McKenna, S.E. / Kimber, M.S. / Seah, S.Y.K.
CitationJournal: Biochemistry / Year: 2013
Title: Characterization of an Aldolase-Dehydrogenase Complex from the Cholesterol Degradation Pathway of Mycobacterium tuberculosis.
Authors: Carere, J. / McKenna, S.E. / Kimber, M.S. / Seah, S.Y.
History
DepositionMar 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Dec 25, 2013Group: Database references
Revision 1.3Sep 20, 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_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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_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: 4-hydroxy-2-oxovalerate aldolase
B: Acetaldehyde dehydrogenase
C: 4-hydroxy-2-oxovalerate aldolase
D: Acetaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,9239
Polymers137,6144
Non-polymers3095
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-57 kcal/mol
Surface area41900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.690, 142.690, 148.170
Angle α, β, γ (deg.)90.00, 95.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-422-

HOH

21C-590-

HOH

31D-476-

HOH

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein 4-hydroxy-2-oxovalerate aldolase / HOA / 4-hydroxy-2-keto-pentanoic acid aldolase / 4-hydroxy-2-oxopentanoate aldolase


Mass: 36487.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Co-expressed with HsaG on the same plasmid / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: HRv37 / Gene: Rv3534c, MT3638 / Plasmid: pTIP-QC1-His / Production host: Rhodococcus jostii (bacteria) / Strain (production host): RHA1
References: UniProt: P71867, UniProt: P9WMK5*PLUS, 4-hydroxy-2-oxovalerate aldolase
#2: Protein Acetaldehyde dehydrogenase / Acetaldehyde dehydrogenase [acetylating]


Mass: 32319.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Co-expressed with HsaF on the same plasmid / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: HRv37 / Gene: mhpF, Rv3535c, MT3639 / Plasmid: pTIP-QC1-His / Production host: Rhodococcus jostii (bacteria) / Strain (production host): RHA1
References: UniProt: P71866, UniProt: P9WQH3*PLUS, acetaldehyde dehydrogenase (acetylating)

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Non-polymers , 4 types, 358 molecules

#3: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 18% PEG 4000, 0.2 M Magnesium chloride, 0.1 M Tris, 10% glycerol and 10 mM sodium oxalate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 11, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.93→45.9 Å / Num. all: 108006 / Num. obs: 105918 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.93→1.98 Å / % possible all: 95

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Processing

Software
NameVersionClassification
MxDXdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model based on 1NVM

1nvm


Resolution: 1.93→45.889 Å / SU ML: 0.21 / Isotropic thermal model: Isotropic, TLS / σ(F): 1.99 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 5296 5 %RANDOM
Rwork0.174 ---
all0.1757 108006 --
obs0.1757 105899 98.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→45.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9413 0 15 353 9781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069587
X-RAY DIFFRACTIONf_angle_d0.99513025
X-RAY DIFFRACTIONf_dihedral_angle_d13.1553473
X-RAY DIFFRACTIONf_chiral_restr0.0691509
X-RAY DIFFRACTIONf_plane_restr0.0051723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.95190.40571690.35143220X-RAY DIFFRACTION95
1.9519-1.97480.34461730.33683282X-RAY DIFFRACTION95
1.9748-1.99890.32341710.32123257X-RAY DIFFRACTION96
1.9989-2.02420.33241710.30173238X-RAY DIFFRACTION96
2.0242-2.05090.28491730.28883288X-RAY DIFFRACTION96
2.0509-2.0790.29061730.26373293X-RAY DIFFRACTION97
2.079-2.10870.30381730.25453280X-RAY DIFFRACTION96
2.1087-2.14010.27261720.24483279X-RAY DIFFRACTION97
2.1401-2.17360.29691750.23453315X-RAY DIFFRACTION97
2.1736-2.20920.26441750.21323331X-RAY DIFFRACTION97
2.2092-2.24730.22861740.20343304X-RAY DIFFRACTION98
2.2473-2.28820.24041750.19733319X-RAY DIFFRACTION98
2.2882-2.33220.24731780.18833383X-RAY DIFFRACTION98
2.3322-2.37980.21241740.17833302X-RAY DIFFRACTION98
2.3798-2.43150.23611780.17483379X-RAY DIFFRACTION98
2.4315-2.48810.22631780.17893387X-RAY DIFFRACTION98
2.4881-2.55030.22881770.17793356X-RAY DIFFRACTION99
2.5503-2.61930.23541770.1733357X-RAY DIFFRACTION99
2.6193-2.69630.20991790.17153399X-RAY DIFFRACTION99
2.6963-2.78330.23351770.16943373X-RAY DIFFRACTION100
2.7833-2.88280.2251800.17633421X-RAY DIFFRACTION100
2.8828-2.99820.21541800.1683411X-RAY DIFFRACTION100
2.9982-3.13460.19551790.16723404X-RAY DIFFRACTION100
3.1346-3.29980.18921810.16713438X-RAY DIFFRACTION100
3.2998-3.50650.21651780.16053388X-RAY DIFFRACTION99
3.5065-3.77710.18461810.15053427X-RAY DIFFRACTION100
3.7771-4.1570.1661790.14683415X-RAY DIFFRACTION100
4.157-4.7580.15481800.13653410X-RAY DIFFRACTION100
4.758-5.99250.18451810.16283451X-RAY DIFFRACTION100
5.9925-45.90170.16741850.14673496X-RAY DIFFRACTION100
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)
16.6701-0.8372-0.39892.0283-0.09165.50880.2621-0.8302-0.14130.1612-0.040.1764-0.4557-0.5608-0.22231.15230.1329-0.40240.5943-0.08440.64121.714848.4753212.8593
23.6375-0.5122-0.94764.68770.71550.7430.0521-0.0656-1.0278-0.01060.0330.1881.19260.0440.0020.98540.0693-0.18140.3446-0.05980.71613.8933-57.7909154.8679
31.050.3210.3272.03610.85531.2085-0.2156-0.12880.16660.23440.1259-0.2793-0.38120.05890.08750.97450.1687-0.35080.3931-0.11220.57877.53435.9956191.3277
42.14610.8944-0.43582.9689-0.26493.6753-0.0460.1899-0.186-0.20190.08680.17710.33390.0544-0.03710.2490.063-0.05460.2106-0.0660.28442.3968-32.1706152.8724
50.8914-0.1450.20861.89150.1211.1157-0.1875-0.15780.02110.37040.11980.1151-0.2363-0.10740.0530.62280.2073-0.14510.3509-0.06670.4224-4.258911.7654186.3969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND ( RESID 3:124 OR RESID 280:298 ) )B3 - 124
2X-RAY DIFFRACTION1( CHAIN B AND ( RESID 3:124 OR RESID 280:298 ) )B280 - 298
3X-RAY DIFFRACTION2( CHAIN D AND ( RESID 3:124 OR RESID 280:298 ) )D3 - 124
4X-RAY DIFFRACTION2( CHAIN D AND ( RESID 3:124 OR RESID 280:298 ) )D280 - 298
5X-RAY DIFFRACTION3( CHAIN B AND RESID 125:279 )B125 - 279
6X-RAY DIFFRACTION4( CHAIN D AND RESID 125:279 )D125 - 279
7X-RAY DIFFRACTION5( CHAIN A AND RESID 4:341 )A4 - 341

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