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

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Basic information

Entry
Database: PDB / ID: 4ply
TitleCrystal structure of ancestral apicomplexan malate dehydrogenase with malate.
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 / PYRUVIC ACID / L-lactate dehydrogenase
Similarity search - Component
Biological speciesApicomplexa (apicomplexans)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.2Jul 30, 2014Group: Database references
Revision 1.3Sep 24, 2014Group: Structure summary
Revision 1.4Oct 1, 2014Group: Database references
Revision 1.5Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
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_oper_list.symmetry_operation
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 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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
F: malate dehydrogenase
E: malate dehydrogenase
G: malate dehydrogenase
H: malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,52422
Polymers291,6728
Non-polymers5,85214
Water12,791710
1
B: malate dehydrogenase
A: malate dehydrogenase
C: malate dehydrogenase
D: malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,76211
Polymers145,8364
Non-polymers2,9267
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19870 Å2
ΔGint-98 kcal/mol
Surface area40510 Å2
MethodPISA
2
F: malate dehydrogenase
E: malate dehydrogenase
G: malate dehydrogenase
H: malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,76211
Polymers145,8364
Non-polymers2,9267
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20280 Å2
ΔGint-96 kcal/mol
Surface area39950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.311, 90.688, 136.304
Angle α, β, γ (deg.)90.010, 90.010, 71.440
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
malate dehydrogenase


Mass: 36458.961 Da / Num. of mol.: 8
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.: 8 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical
ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / 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: 50.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20mg/mL protein with 2mM NADH/L-malate; 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
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 1.9→50 Å / Num. obs: 198358 / % possible obs: 93.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 9.2
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 3.5 % / Rmerge(I) obs: 2.23 / Mean I/σ(I) obs: 0.56 / % possible all: 71.5

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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: 1.9→45.435 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.69 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2381 3637 0.95 %
Rwork0.1894 380157 -
obs0.1904 383647 90.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73 Å2 / Biso mean: 39.9309 Å2 / Biso min: 17.8 Å2
Refinement stepCycle: final / Resolution: 1.9→45.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18773 0 388 710 19871
Biso mean--39.58 37.25 -
Num. residues----2484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319563
X-RAY DIFFRACTIONf_angle_d0.7426554
X-RAY DIFFRACTIONf_chiral_restr0.0253115
X-RAY DIFFRACTIONf_plane_restr0.0033357
X-RAY DIFFRACTIONf_dihedral_angle_d14.4737292
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.93140.4403690.41647358742735
1.9314-1.96650.42811060.3811110551116152
1.9665-2.00430.35631440.3635145991474369
2.0043-2.04520.34981650.3489190041916989
2.0452-2.08970.35441650.3309198101997594
2.0897-2.13820.32781850.3134202002038595
2.1382-2.19170.3321710.2908204092058095
2.1917-2.25090.33891900.293202812047196
2.2509-2.31720.31691840.2609203922057696
2.3172-2.39190.26281880.253204842067296
2.3919-2.47740.28611820.2399205182070096
2.4774-2.57650.28361920.2284204642065696
2.5765-2.69370.29951780.2184205322071097
2.6937-2.83560.27161800.2073206342081497
2.8356-3.01320.27621880.1903205932078197
3.0132-3.24560.25911900.1727207142090497
3.2456-3.57170.19011840.1569206122079697
3.5717-4.08750.16921920.137207712096398
4.0875-5.14590.14841810.1221207692095097
5.1459-30.60830.22821930.1467209582115198

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