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

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Basic information

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


L-lactate dehydrogenase (NAD+) activity / lactate 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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / OXAMIC ACID / L-lactate dehydrogenase
Similarity search - Component
Biological speciesApicomplexa (apicomplexans)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.4Dec 24, 2014Group: Database references
Revision 1.5Feb 25, 2015Group: Derived calculations
Revision 1.6Sep 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 1.7Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.8Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)148,85412
Polymers145,8364
Non-polymers3,0188
Water15,493860
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21010 Å2
ΔGint-115 kcal/mol
Surface area39530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.527, 136.311, 90.238
Angle α, β, γ (deg.)90.000, 108.780, 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-OXM / OXAMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 860 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20mg/mL protein with 2mM NADH/L-oxamate; 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: 1.6→50 Å / Num. obs: 350147 / % possible obs: 98.5 % / Redundancy: 2.5 % / Biso Wilson estimate: 26.91 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.66
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 2.4 % / Rmerge(I) obs: 2.36 / Mean I/σ(I) obs: 0.41 / % possible all: 97.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
Cootmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HJR

2hjr


Resolution: 1.6→43.432 Å / FOM work R set: 0.7516 / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 4343 1.3 %
Rwork0.1893 330521 -
obs0.1897 334864 94.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.73 Å2 / Biso mean: 33.41 Å2 / Biso min: 14.08 Å2
Refinement stepCycle: final / Resolution: 1.6→43.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9544 0 200 860 10604
Biso mean--29.13 42.35 -
Num. residues----1274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019980
X-RAY DIFFRACTIONf_angle_d1.27313578
X-RAY DIFFRACTIONf_chiral_restr0.0571599
X-RAY DIFFRACTIONf_plane_restr0.0061723
X-RAY DIFFRACTIONf_dihedral_angle_d16.3723686
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.6170.4549650.49544983504842
1.617-1.63610.4764980.46448009810769
1.6361-1.6560.44421230.44589673979682
1.656-1.6770.43981550.441102141036988
1.677-1.6990.43211270.4224105521067990
1.699-1.72230.45291570.41109701112794
1.7223-1.74690.44351490.381114071155697
1.7469-1.7730.36811470.3651115051165299
1.773-1.80070.3611570.3469116351179299
1.8007-1.83020.35431510.32511150011651100
1.8302-1.86180.36821590.31751178311942100
1.8618-1.89560.32611530.3055115271168099
1.8956-1.93210.33291570.2874115901174799
1.9321-1.97150.31971560.26111168611842100
1.9715-2.01440.27611460.2495115581170499
2.0144-2.06130.24561550.2425116181177399
2.0613-2.11280.2561430.2237115401168399
2.1128-2.16990.25951620.2083115451170799
2.1699-2.23380.27611540.2025116171177199
2.2338-2.30590.26581550.1998114641161998
2.3059-2.38830.27041560.1956115781173499
2.3883-2.48390.23621450.1883115261167199
2.4839-2.5970.25621480.1769115111165998
2.597-2.73380.19641530.173114331158698
2.7338-2.90510.21791390.1745114061154598
2.9051-3.12930.24141410.1665114251156697
3.1293-3.44410.18741520.1552112251137796
3.4441-3.94220.17421350.1406111681130395
3.9422-4.96570.12751570.1197114011155897
4.9657-43.44760.13641480.1403114721162098

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