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- PDB-6vdh: Crystal structure of ancestral apicomplexan lactate dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 6vdh
TitleCrystal structure of ancestral apicomplexan lactate dehydrogenase in alternate dimer configuration with sulfate.
Componentslactate dehydrogenase
KeywordsOXIDOREDUCTASE / Nucleotide Binding / Rossman Fold / Ancestral Reconstruction
Function / homologyL-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesApicomplexa sp. (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTheobald, D.L. / Wirth, J.D. / Classen, S. / Perlmutter, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM096053 United States
CitationJournal: To Be Published
Title: Mechanism of Bifunctionality in an Ancestral Apicomplexan Malate/Lactate Dehydrogenase
Authors: Theobald, D.L. / Wirth, J.D. / Classen, S. / Perlmutter, N.
History
DepositionDec 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: lactate dehydrogenase
B: lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0034
Polymers71,8112
Non-polymers1922
Water5,819323
1
A: lactate dehydrogenase
B: lactate dehydrogenase
hetero molecules

A: lactate dehydrogenase
B: lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,0068
Polymers143,6224
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area17220 Å2
ΔGint-135 kcal/mol
Surface area42850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.380, 105.440, 151.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein lactate dehydrogenase


Mass: 35905.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Ancestral apicomplexan lactate dehydrogenase in alternate dimer conformation with sulfate bound
Source: (gene. exp.) Apicomplexa sp. (eukaryote) / Plasmid: pET24a(+) / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20mg/mL protein, 2mM NADH4; well solution: 5% v/v 2-Propanol, 2.5M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.115866 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115866 Å / Relative weight: 1
ReflectionResolution: 1.68→45.53 Å / Num. obs: 86980 / % possible obs: 88.9 % / Redundancy: 5.92 % / Biso Wilson estimate: 30.34 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.102 / Χ2: 0.86 / Net I/σ(I): 3.66
Reflection shellResolution: 1.68→1.79 Å / Redundancy: 3.18 % / Mean I/σ(I) obs: 0.18 / Num. unique obs: 18335 / CC1/2: 0.071 / Rrim(I) all: 5.295 / % possible all: 62.6

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PLG

4plg


Resolution: 1.85→45.53 Å / SU ML: 0.3457 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.0699
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2362 1533 2.34 %
Rwork0.2095 63961 -
obs0.2101 65494 92.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.49 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4726 0 10 323 5059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00374812
X-RAY DIFFRACTIONf_angle_d0.5926512
X-RAY DIFFRACTIONf_chiral_restr0.046763
X-RAY DIFFRACTIONf_plane_restr0.0036835
X-RAY DIFFRACTIONf_dihedral_angle_d4.6525661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.910.57191080.52024194X-RAY DIFFRACTION67.96
1.91-1.980.61721200.57495093X-RAY DIFFRACTION82.28
1.98-2.060.26371490.23666240X-RAY DIFFRACTION99.92
2.06-2.150.25981440.21736249X-RAY DIFFRACTION99.95
2.15-2.260.37071190.32974914X-RAY DIFFRACTION79.33
2.26-2.410.27681380.2295659X-RAY DIFFRACTION89.99
2.41-2.590.24781460.19336237X-RAY DIFFRACTION99.98
2.59-2.850.22341450.19076289X-RAY DIFFRACTION100
2.85-3.270.18871580.19056262X-RAY DIFFRACTION100
3.27-4.110.20451420.18476298X-RAY DIFFRACTION98.94
4.11-45.530.20121640.17436526X-RAY DIFFRACTION99.78

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