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- PDB-4plv: Crystal structure of ancestral apicomplexan malate dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 4plv
TitleCrystal structure of ancestral apicomplexan malate dehydrogenase with lactate.
Componentsmalate dehydrogenase
KeywordsOXIDOREDUCTASE / Ancestral Sequence Reconstruction / Dehydrogenase / Apicomplexa / Specificity
Function / homology
Function and homology information


L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / pyruvate metabolic process / nucleotide binding
Similarity search - Function
Malate dehydrogenase, type 3 / 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 ...Malate dehydrogenase, type 3 / 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
(2S)-2-HYDROXYPROPANOIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / L-lactate dehydrogenase
Similarity search - Component
Biological speciesApicomplexa (apicomplexans)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBoucher, J.I. / Jacobowitz, J.R. / Beckett, B.C. / Classen, S. / Theobald, D.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM096053 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM094468 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM105404 United States
CitationJournal: Elife / Year: 2014
Title: An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases.
Authors: Boucher, J.I. / Jacobowitz, J.R. / Beckett, B.C. / Classen, S. / Theobald, D.L.
History
DepositionMay 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Structure summary
Revision 1.3Oct 1, 2014Group: Database references
Revision 1.4Feb 25, 2015Group: Derived calculations
Revision 1.5Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.6Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.8Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: malate dehydrogenase
B: malate dehydrogenase
C: malate dehydrogenase
D: malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,85812
Polymers145,8364
Non-polymers3,0228
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19380 Å2
ΔGint-110 kcal/mol
Surface area39320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.336, 136.329, 90.810
Angle α, β, γ (deg.)90.000, 108.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
malate dehydrogenase


Mass: 36458.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apicomplexa (apicomplexans) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 (pLysS) / References: UniProt: A0A075B5H0*PLUS
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical
ChemComp-2OP / (2S)-2-HYDROXYPROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 50.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20mg/mL protein with 2mM NADH/L-lactate; well solution: 20% (w/v) PEG-1500, 0.1M HEPES, pH7.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.115866 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115866 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 112107 / % possible obs: 96 % / Redundancy: 4.3 % / Biso Wilson estimate: 9.91 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.3
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 3.1 % / Rmerge(I) obs: 2.14 / Mean I/σ(I) obs: 0.54 / % possible all: 78.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HJR

2hjr


Resolution: 1.85→43.388 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2449 3266 1.58 %
Rwork0.2018 202829 -
obs0.2025 206095 89.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.6 Å2 / Biso mean: 40.1117 Å2 / Biso min: 18.91 Å2
Refinement stepCycle: final / Resolution: 1.85→43.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9348 0 200 461 10009
Biso mean--41.12 42.23 -
Num. residues----1248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089744
X-RAY DIFFRACTIONf_angle_d1.09813254
X-RAY DIFFRACTIONf_chiral_restr0.0431572
X-RAY DIFFRACTIONf_plane_restr0.0051676
X-RAY DIFFRACTIONf_dihedral_angle_d14.7773578
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.8760.406400.42712226226623
1.876-1.90530.523460.47262881292729
1.9053-1.93660.5265720.47024625469747
1.9366-1.970.37031350.3777928806380
1.97-2.00580.36691440.36418928907291
2.0058-2.04440.37861520.35529580973296
2.0444-2.08610.35381570.35329599975698
2.0861-2.13140.34681520.314598581001098
2.1314-2.1810.34261590.29499686984599
2.181-2.23560.33621550.3079712986799
2.2356-2.2960.38011670.31819746991399
2.296-2.36360.30721530.25059819997299
2.3636-2.43980.30951560.24179797995399
2.4398-2.5270.26731590.22949810996999
2.527-2.62820.28391580.21759758991699
2.6282-2.74780.25781550.211498571001299
2.7478-2.89260.2451500.206498259975100
2.8926-3.07380.29281620.2014987910041100
3.0738-3.31110.29681580.1866986210020100
3.3111-3.64410.20571680.1709987910047100
3.6441-4.17110.19751560.145598379993100
4.1711-5.25370.1541600.126398349994100
5.2537-43.40020.15561520.1427990310055100

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