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- PDB-4uul: Apo trichomonas vaginalis lactate dehydrogenase L91R -

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Basic information

Entry
Database: PDB / ID: 4uul
TitleApo trichomonas vaginalis lactate dehydrogenase L91R
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: 1.28 Å
AuthorsSteindel, P.A. / Chen, E.H. / L Theobald, D.
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)75,9972
Polymers75,9972
Non-polymers00
Water18,1051005
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-24.1 kcal/mol
Surface area28270 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: 37998.348 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRICHOMONAS VAGINALIS (eukaryote) / Plasmid: PET-21B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O96445, L-lactate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1005 / 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
Details: 21 MG/ML PROTEIN, 100 MM HEPES PH 7.0, 10% 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 CCD / 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: 1.3→44.7 Å / Num. obs: 175089 / % possible obs: 90.3 % / Observed criterion σ(I): 2.61 / Redundancy: 13.1 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.2
Reflection shellResolution: 1.28→1.31 Å / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.61 / % possible all: 47.5

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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: 1.28→30.712 Å / SU ML: 0.1 / σ(F): 1.99 / Phase error: 16.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1545 8784 5 %
Rwork0.1293 --
obs0.1306 175050 90.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.4 Å2
Refinement stepCycle: LAST / Resolution: 1.28→30.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5240 0 0 1005 6245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135614
X-RAY DIFFRACTIONf_angle_d1.4747667
X-RAY DIFFRACTIONf_dihedral_angle_d12.6752039
X-RAY DIFFRACTIONf_chiral_restr0.099844
X-RAY DIFFRACTIONf_plane_restr0.01993
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2798-1.29430.26251220.20812373X-RAY DIFFRACTION39
1.2943-1.30960.26541680.20183153X-RAY DIFFRACTION52
1.3096-1.32550.20081900.16843607X-RAY DIFFRACTION59
1.3255-1.34230.20072200.16433942X-RAY DIFFRACTION65
1.3423-1.360.22482220.15664308X-RAY DIFFRACTION71
1.36-1.37860.21352460.16764728X-RAY DIFFRACTION77
1.3786-1.39830.20082780.14125102X-RAY DIFFRACTION84
1.3983-1.41920.17632900.13285642X-RAY DIFFRACTION92
1.4192-1.44130.17553070.12845886X-RAY DIFFRACTION97
1.4413-1.4650.15973250.12566010X-RAY DIFFRACTION98
1.465-1.49020.16293230.1216076X-RAY DIFFRACTION99
1.4902-1.51730.15413210.11235991X-RAY DIFFRACTION99
1.5173-1.54650.1633100.11586018X-RAY DIFFRACTION99
1.5465-1.57810.14573300.10766037X-RAY DIFFRACTION99
1.5781-1.61240.14053340.10416093X-RAY DIFFRACTION99
1.6124-1.64990.14092930.10836064X-RAY DIFFRACTION99
1.6499-1.69110.15373300.11156090X-RAY DIFFRACTION99
1.6911-1.73690.15473440.11546013X-RAY DIFFRACTION99
1.7369-1.7880.15533110.1166117X-RAY DIFFRACTION99
1.788-1.84570.15213060.12096108X-RAY DIFFRACTION99
1.8457-1.91160.1483310.12656118X-RAY DIFFRACTION99
1.9116-1.98820.16673120.1346138X-RAY DIFFRACTION100
1.9882-2.07860.16993250.12636106X-RAY DIFFRACTION100
2.0786-2.18820.13383370.11986131X-RAY DIFFRACTION100
2.1882-2.32520.15393210.11726112X-RAY DIFFRACTION100
2.3252-2.50470.13553220.11346182X-RAY DIFFRACTION100
2.5047-2.75660.13123180.12096163X-RAY DIFFRACTION100
2.7566-3.15510.15573310.13356164X-RAY DIFFRACTION100
3.1551-3.97380.15673240.13396197X-RAY DIFFRACTION99
3.9738-30.72060.15972930.1575597X-RAY DIFFRACTION88

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