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- PDB-4uum: Apo trichomonas vaginalis lactate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 4uum
TitleApo trichomonas vaginalis lactate dehydrogenase
ComponentsL-LACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


malate dehydrogenase activity / malate dehydrogenase / malate metabolic process / L-lactate dehydrogenase (NAD+) activity / nucleotide binding
Similarity search - Function
Lactate dehydrogenase, protist / Malate dehydrogenase, type 2 / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal ...Lactate dehydrogenase, protist / Malate dehydrogenase, type 2 / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
malate dehydrogenase
Similarity search - Component
Biological speciesTRICHOMONAS VAGINALIS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.368 Å
AuthorsSteindel, P.A. / Chen, E.H. / Theobald, D.L.
CitationJournal: Protein Sci. / Year: 2016
Title: Gradual Neofunctionalization in the Convergent Evolution of Trichomonad Lactate and Malate Dehydrogenases.
Authors: Steindel, P.A. / Chen, E.H. / Wirth, J.D. / Theobald, D.L.
History
DepositionJul 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Jul 6, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-LACTATE DEHYDROGENASE
B: L-LACTATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)75,9092
Polymers75,9092
Non-polymers00
Water18,8801048
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-24.3 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.570, 59.610, 86.490
Angle α, β, γ (deg.)90.00, 116.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein L-LACTATE DEHYDROGENASE / LACTATE DEHYDROGENASE


Mass: 37954.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRICHOMONAS VAGINALIS (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O96445, L-lactate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1048 / 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: 2.49 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7.6
Details: 44 MG/ML PROTEIN, 100 MM HEPES PH 7.6, 8.3% PEG-6000, 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.4→44.7 Å / Num. obs: 145693 / % possible obs: 91.5 % / Observed criterion σ(I): 1.42 / Redundancy: 6.66 % / Biso Wilson estimate: 15.99 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.8
Reflection shellResolution: 1.37→1.4 Å / Mean I/σ(I) obs: 1.42 / % possible all: 48.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL BASED ON PDB ENTRY 5MDH

5mdh


Resolution: 1.368→44.653 Å / SU ML: 0.09 / σ(F): 1.99 / Phase error: 13.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1402 7307 5 %
Rwork0.1279 --
obs0.1286 145673 91.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.4 Å2
Refinement stepCycle: LAST / Resolution: 1.368→44.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5240 0 0 1048 6288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085592
X-RAY DIFFRACTIONf_angle_d1.1777636
X-RAY DIFFRACTIONf_dihedral_angle_d12.1682032
X-RAY DIFFRACTIONf_chiral_restr0.076845
X-RAY DIFFRACTIONf_plane_restr0.007988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3681-1.38370.28321080.24842119X-RAY DIFFRACTION42
1.3837-1.40.22911460.20552715X-RAY DIFFRACTION54
1.4-1.4170.20261750.19662998X-RAY DIFFRACTION60
1.417-1.4350.21071760.18233303X-RAY DIFFRACTION67
1.435-1.45390.19681960.1743709X-RAY DIFFRACTION74
1.4539-1.47380.1932030.15734099X-RAY DIFFRACTION81
1.4738-1.49480.17052400.1414357X-RAY DIFFRACTION87
1.4948-1.51720.14892400.13364616X-RAY DIFFRACTION92
1.5172-1.54090.14582480.12844895X-RAY DIFFRACTION97
1.5409-1.56610.1372790.12395004X-RAY DIFFRACTION100
1.5661-1.59310.1372540.11514963X-RAY DIFFRACTION100
1.5931-1.62210.13182820.11065038X-RAY DIFFRACTION100
1.6221-1.65330.12482450.10735058X-RAY DIFFRACTION100
1.6533-1.68710.13152710.10794984X-RAY DIFFRACTION100
1.6871-1.72370.1342690.10774998X-RAY DIFFRACTION100
1.7237-1.76380.12512590.10875032X-RAY DIFFRACTION100
1.7638-1.8080.11942750.11195033X-RAY DIFFRACTION100
1.808-1.85680.13612430.11845002X-RAY DIFFRACTION100
1.8568-1.91150.132830.12325047X-RAY DIFFRACTION100
1.9115-1.97320.13642520.12914992X-RAY DIFFRACTION100
1.9732-2.04370.15012690.12615031X-RAY DIFFRACTION100
2.0437-2.12550.13762700.12155039X-RAY DIFFRACTION100
2.1255-2.22230.12142650.11745042X-RAY DIFFRACTION100
2.2223-2.33940.14332680.11775041X-RAY DIFFRACTION100
2.3394-2.4860.13262750.11775054X-RAY DIFFRACTION100
2.486-2.67790.13252660.12335030X-RAY DIFFRACTION100
2.6779-2.94730.14742500.1295057X-RAY DIFFRACTION100
2.9473-3.37370.13122720.12945092X-RAY DIFFRACTION100
3.3737-4.250.13942700.12845100X-RAY DIFFRACTION100
4.25-44.67650.14722580.14414918X-RAY DIFFRACTION94

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