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- PDB-4uun: Trichomonas vaginalis lactate dehydrogenase in complex with NADH -

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Basic information

Entry
Database: PDB / ID: 4uun
TitleTrichomonas vaginalis lactate dehydrogenase in complex with NADH
ComponentsL-LACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


L-malate dehydrogenase (NAD+) activity / L-lactate dehydrogenase / malate metabolic process / oxaloacetate metabolic process / L-lactate dehydrogenase (NAD+) activity / 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 / L-lactate dehydrogenase
Similarity search - Component
Biological speciesTRICHOMONAS VAGINALIS (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 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 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)77,2404
Polymers75,9092
Non-polymers1,3312
Water17,366964
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-39 kcal/mol
Surface area28290 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) / Plasmid: PET-21B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O96445, L-lactate dehydrogenase
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 964 / 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: 6.8
Details: 20 MG/ML PROTEIN, 100 MM HEPES PH 6.8, 8% PEG-6000, 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
DetectorType: OXFORD / Detector: CCD / Date: Sep 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.78→46.3 Å / Num. obs: 67400 / % possible obs: 89.9 % / Observed criterion σ(I): 1.45 / Redundancy: 3.23 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.18
Reflection shellResolution: 1.78→1.83 Å / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 1.17 / % possible all: 37.5

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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: 1.78→45.829 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1904 3233 5 %
Rwork0.154 --
obs-64666 89.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.7 Å2
Refinement stepCycle: LAST / Resolution: 1.78→45.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5250 0 88 964 6302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055738
X-RAY DIFFRACTIONf_angle_d1.0637854
X-RAY DIFFRACTIONf_dihedral_angle_d12.2792098
X-RAY DIFFRACTIONf_chiral_restr0.06867
X-RAY DIFFRACTIONf_plane_restr0.0051005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7831-1.84680.3411450.29942726X-RAY DIFFRACTION40
1.8468-1.92080.29042450.26364760X-RAY DIFFRACTION70
1.9208-2.00820.25863160.21296121X-RAY DIFFRACTION90
2.0082-2.11410.22333680.19036780X-RAY DIFFRACTION99
2.1141-2.24650.20643480.16356794X-RAY DIFFRACTION100
2.2465-2.41990.20273680.15286786X-RAY DIFFRACTION99
2.4199-2.66350.18793640.14956791X-RAY DIFFRACTION99
2.6635-3.04880.18323500.15216833X-RAY DIFFRACTION100
3.0488-3.84090.16973600.13186843X-RAY DIFFRACTION99
3.8409-45.84430.15743690.12686999X-RAY DIFFRACTION99
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)
10.75880.04760.11040.2549-0.13160.22370.01390.16660.1876-0.0567-0.0411-0.03440.01610.0174-0.02350.1274-0.00340.00830.14260.04870.116623.50285.60629.3511
20.98090.0105-0.09690.4015-0.24110.4793-0.0069-0.0954-0.1042-0.0292-0.0666-0.14030.07170.0989-0.0210.13940.00330.00030.17350.03970.130334.519-9.320523.1669
30.8384-0.1831-0.08380.2231-0.08080.07270.0258-0.0991-0.30730.03260.00090.03490.0102-0.0111-0.00110.1405-0.017-0.01130.11790.00860.1533-0.1943-15.737121.759
41.1176-0.1357-0.13590.6199-0.07070.27450.03880.00810.20520.034-0.01220.1049-0.0791-0.03420.0410.12190.00090.0090.0853-0.01930.1239-10.90462.992615.8749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2 THROUGH 153 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 154 THROUGH 336 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 2 THROUGH 153 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 154 THROUGH 338 )

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