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- PDB-4plc: Crystal structure of ancestral apicomplexan lactate dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 4plc
TitleCrystal structure of ancestral apicomplexan lactate dehydrogenase with malate.
Componentslactate 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / PYRUVIC ACID / L-lactate dehydrogenase
Similarity search - Component
Biological speciesApicomplexa (apicomplexans)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 16, 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 1.4Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / 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_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.country ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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
A: lactate dehydrogenase
B: lactate dehydrogenase
C: lactate dehydrogenase
D: lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,66012
Polymers146,6504
Non-polymers3,0108
Water24,6081366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22720 Å2
ΔGint-74 kcal/mol
Surface area41480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.369, 134.369, 159.025
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
lactate dehydrogenase


Mass: 36662.469 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: A0A075B5G8*PLUS
#2: Chemical
ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O3
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1366 / 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: 2.92 Å3/Da / Density % sol: 57.92 %
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,-h-k,-l / Fraction: 0.5
ReflectionResolution: 1.5→50 Å / Num. obs: 258762 / % possible obs: 99.5 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.8
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.368 / Mean I/σ(I) obs: 0.93 / % possible all: 96.9

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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 / Resolution: 1.5→46.955 Å / FOM work R set: 0.9115 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 15.77 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.152 2016 0.78 %
Rwork0.1242 256525 -
obs0.1339 258762 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 221.33 Å2 / Biso mean: 23.95 Å2 / Biso min: 7.79 Å2
Refinement stepCycle: final / Resolution: 1.5→46.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9904 0 318 1366 11588
Biso mean--27.66 39.06 -
Num. residues----1296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510399
X-RAY DIFFRACTIONf_angle_d0.98214062
X-RAY DIFFRACTIONf_chiral_restr0.0491621
X-RAY DIFFRACTIONf_plane_restr0.0041784
X-RAY DIFFRACTIONf_dihedral_angle_d14.9534005
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.53760.28171440.2514179241806897
1.5376-1.57920.23361440.2237183311847599
1.5792-1.62560.20361460.2076182811842799
1.6256-1.67810.20691480.1937183721852099
1.6781-1.73810.18421410.1774182731841499
1.7381-1.80760.17931440.1679183321847699
1.8076-1.88990.18261410.157183291847099
1.8899-1.98950.19431450.1524183291847499
1.9895-2.11410.17061440.1498183211846599
2.1141-2.27720.17221430.1409183931853699
2.2772-2.50620.13941400.1334183191845999
2.5062-2.86840.15291430.1197183891853299
2.8684-3.61240.15291440.1101183991854399
3.6124-25.77640.12141490.0977185331868299
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)
10.34390.004-0.00620.22140.04090.105-0.0258-0.0688-0.0850.03540.01760.02160.0326-0.0373-0.00050.14-0.0008-0.00380.11070.01620.10542.755422.749416.9617
20.335-0.0198-0.05130.1739-0.02990.2843-0.0206-0.05040.007-0.00250.0024-0.03590.01230.0393-0.00070.10760.0113-0.01430.08940.00420.097521.902933.142113.2605
30.406-0.05750.28110.18580.05670.1982-0.06510.18920.1698-0.03660.03180.0525-0.01460.0399-0.06230.1341-0.0243-0.02350.14970.04090.13326.789752.8763-21.8968
40.40580.010.01890.21120.05850.1864-0.03980.09940.06110.00260.026-0.0612-0.00860.0461-0.00150.1055-0.0143-0.0030.12350.01320.120724.866143.506-13.5143
50.29770.0003-0.03120.16680.00170.1226-0.01390.1008-0.1078-0.03050.0091-0.02790.03590.0406-0.00340.1532-0.0012-0.00790.1392-0.02590.1116-0.455623.406-23.3858
60.28350.0476-0.09870.1454-0.00680.283-0.02090.08570.0061-0.00430.01170.03620.029-0.06180.00010.1309-0.0171-0.01730.1383-0.00470.1086-20.088532.7303-19.2157
70.36070.01590.28350.089-0.07910.1403-0.0665-0.14860.13620.02290.0359-0.049-0.0217-0.029-0.00260.13330.021-0.02440.1194-0.02580.1356-5.85952.101116.2847
80.3222-0.00120.00050.1723-0.0880.2775-0.0179-0.0570.0390.02290.02290.04280.0061-0.061800.11260.00470.00180.1192-0.00180.1333-23.483642.28557.7313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 153 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 154 through 328 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 5 through 153 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 154 through 328 )B0
5X-RAY DIFFRACTION5chain 'C' and (resid 5 through 153 )C0
6X-RAY DIFFRACTION6chain 'C' and (resid 154 through 328 )C0
7X-RAY DIFFRACTION7chain 'D' and (resid 5 through 153 )D0
8X-RAY DIFFRACTION8chain 'D' and (resid 154 through 328 )D0

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