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- PDB-5a1t: Trichomonas vaginalis lactate dehydrogenase in complex with NADH ... -

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Basic information

Entry
Database: PDB / ID: 5a1t
TitleTrichomonas vaginalis lactate dehydrogenase in complex with NADH and oxamate
ComponentsL-LACTATE DEHYDROGENASELactate dehydrogenase
KeywordsOXIDOREDUCTASE / LACTATE DEHYDROGENASE
Function / homology
Function and homology information


L-malate dehydrogenase activity / malate metabolic process / L-lactate dehydrogenase / L-lactate dehydrogenase activity / oxaloacetate metabolic process / NADH metabolic process / tricarboxylic acid cycle / 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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / OXAMIC ACID / L-lactate dehydrogenase
Similarity search - Component
Biological speciesTRICHOMONAS VAGINALIS (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 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
DepositionMay 5, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 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 ...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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: L-LACTATE DEHYDROGENASE
B: L-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4186
Polymers75,9092
Non-polymers1,5094
Water11,800655
1
A: L-LACTATE DEHYDROGENASE
hetero molecules

A: L-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4186
Polymers75,9092
Non-polymers1,5094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area6410 Å2
ΔGint-29.9 kcal/mol
Surface area25500 Å2
MethodPISA
2
B: L-LACTATE DEHYDROGENASE
hetero molecules

B: L-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4186
Polymers75,9092
Non-polymers1,5094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area6610 Å2
ΔGint-27.3 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.120, 82.680, 114.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-2010-

HOH

21B-2010-

HOH

31B-2023-

HOH

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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: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-OXM / OXAMIC ACID / Oxamic acid


Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 655 / 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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growDetails: 0.2 M POTASSIUM SODIUM TARTRATE TETRAHYDRATE, 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 2.0 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OXFORD ENHANCE ULTRA / Wavelength: 1.54
DetectorType: OXFORD / Detector: CCD / Date: Nov 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.97→47 Å / Num. obs: 39768 / % possible obs: 73.1 % / Observed criterion σ(I): 1.31 / Redundancy: 13 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 14.7
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.3 / % possible all: 54.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UUL

4uul


Resolution: 1.97→46.998 Å / SU ML: 0.26 / σ(F): 1.33 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2503 1935 5 %
Rwork0.2013 --
obs0.2037 38882 71.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 1.97→46.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5140 0 100 655 5895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035429
X-RAY DIFFRACTIONf_angle_d0.8127395
X-RAY DIFFRACTIONf_dihedral_angle_d12.0961953
X-RAY DIFFRACTIONf_chiral_restr0.03819
X-RAY DIFFRACTIONf_plane_restr0.003936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.01930.3849950.30321986X-RAY DIFFRACTION54
2.0193-2.07390.8286180.5908284X-RAY DIFFRACTION18
2.0739-2.13490.3904690.24981465X-RAY DIFFRACTION54
2.1349-2.20390.2781770.22483300X-RAY DIFFRACTION91
2.2039-2.28260.2613180.2203388X-RAY DIFFRACTION11
2.2826-2.3740.23761900.20723556X-RAY DIFFRACTION98
2.374-2.4820.28921940.20733625X-RAY DIFFRACTION99
2.482-2.61290.27011910.22083618X-RAY DIFFRACTION99
2.6129-2.77660.2431990.22361889X-RAY DIFFRACTION51
2.7766-2.99090.26591830.21573665X-RAY DIFFRACTION99
2.9909-3.29190.26221990.20113686X-RAY DIFFRACTION100
3.2919-3.7680.26181170.18752332X-RAY DIFFRACTION63
3.768-4.74660.18991770.16543231X-RAY DIFFRACTION86
4.7466-47.01170.22382080.18383922X-RAY DIFFRACTION100

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