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- PDB-4plz: Crystal structure of Plasmodium falciparum lactate dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 4plz
TitleCrystal structure of Plasmodium falciparum lactate dehydrogenase mutant W107fA.
ComponentsL-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / Ancestral Sequence Reconstruction / Dehydrogenase / Apicomplexa / Specificity
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / metal ion 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 / L-lactate dehydrogenase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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 20, 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 2.0Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Non-polymer description / Other / Refinement description / 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_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / software
Item: _chem_comp.formula / _chem_comp.id ..._chem_comp.formula / _chem_comp.id / _chem_comp.name / _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_oper_list.symmetry_operation / _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 2.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Sep 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

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Assembly

Deposited unit
A: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6173
Polymers34,8621
Non-polymers7542
Water9,854547
1
A: L-lactate dehydrogenase
hetero molecules

A: L-lactate dehydrogenase
hetero molecules

A: L-lactate dehydrogenase
hetero molecules

A: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,46812
Polymers139,4504
Non-polymers3,0188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area20310 Å2
ΔGint-99 kcal/mol
Surface area37420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.530, 86.010, 91.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-591-

HOH

21A-708-

HOH

31A-709-

HOH

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Components

#1: Protein L-lactate dehydrogenase / Lactate dehydrogenase


Mass: 34862.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: LDH-P, LDH, ldh / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 (pLysS)
References: UniProt: Q71T02, UniProt: Q27743*PLUS, L-lactate dehydrogenase
#2: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3NO3
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20mg/mL protein with 1.2mM oxamate/2mM NADH; 22% PEG-1000

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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: Dec 18, 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: 1.05→50 Å / Num. obs: 284505 / % possible obs: 99.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 9.15 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 18.9
Reflection shellResolution: 1.05→1.08 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.81 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIXrefinement
Blu-Icedata collection
XDSdata reduction
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T2D

1t2d


Resolution: 1.05→45.72 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1457 3886 1.37 %
Rwork0.1302 280608 -
obs0.1304 284494 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.92 Å2 / Biso mean: 14.663 Å2 / Biso min: 5.78 Å2
Refinement stepCycle: final / Resolution: 1.05→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 50 547 2839
Biso mean--11.2 29.48 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142489
X-RAY DIFFRACTIONf_angle_d1.5883420
X-RAY DIFFRACTIONf_chiral_restr0.075415
X-RAY DIFFRACTIONf_plane_restr0.009437
X-RAY DIFFRACTIONf_dihedral_angle_d15.862944
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.05-1.06280.26971390.23579632977196
1.0628-1.07630.241320.22449851998398
1.0763-1.09050.25191450.206899421008798
1.0905-1.10540.17461370.188399631010099
1.1054-1.12120.17151290.1687100011013099
1.1212-1.13790.21541300.155899751010599
1.1379-1.15570.14611660.142599801014699
1.1557-1.17470.14621260.1377100201014699
1.1747-1.19490.14841360.1356100791021599
1.1949-1.21660.17891420.1303100041014699
1.2166-1.240.13351430.1239100131015699
1.24-1.26540.14331430.120499871013099
1.2654-1.29290.16091270.1135100011012899
1.2929-1.32290.12971510.10951011010261100
1.3229-1.3560.11991300.10741007810208100
1.356-1.39270.131440.1052999410138100
1.3927-1.43370.1221330.10421018310316100
1.4337-1.480.11281510.0991998310134100
1.48-1.53290.12151290.09941007410203100
1.5329-1.59420.13121360.09961007810214100
1.5942-1.66680.1151420.10571005410196100
1.6668-1.75470.13411470.11351010510252100
1.7547-1.86460.15261330.11871014310276100
1.8646-2.00860.13431460.11851002910175100
2.0086-2.21070.12141410.12211004610187100
2.2107-2.53060.1551300.1351009410224100
2.5306-3.18820.14411390.14431007710216100
3.1882-45.76340.15661390.14111011210251100

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