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

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Basic information

Entry
Database: PDB / ID: 4plg
TitleCrystal structure of ancestral apicomplexan lactate dehydrogenase with oxamate.
Componentslactate 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: 1.192 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_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact
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_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,01814
Polymers73,3252
Non-polymers1,69312
Water13,277737
1
A: lactate dehydrogenase
B: lactate dehydrogenase
hetero molecules

A: lactate dehydrogenase
B: lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,03628
Polymers146,6504
Non-polymers3,38624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area24170 Å2
ΔGint-262 kcal/mol
Surface area40690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.680, 143.260, 91.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-570-

HOH

21A-606-

HOH

31A-627-

HOH

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Components

#1: Protein lactate dehydrogenase


Mass: 36662.469 Da / Num. of mol.: 2
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-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3NO3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
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: 1.19→50 Å / Num. obs: 803215 / % possible obs: 87.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 13.27 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 9.17
Reflection shellResolution: 1.19→1.22 Å / Redundancy: 2.1 % / Rmerge(I) obs: 2.89 / Mean I/σ(I) obs: 0.44 / % possible all: 39.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PZF

1pzf


Resolution: 1.192→44.525 Å / FOM work R set: 0.8307 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1875 1991 0.89 %
Rwork0.1671 220474 -
obs0.1673 222465 94.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.82 Å2 / Biso mean: 20.78 Å2 / Biso min: 9.22 Å2
Refinement stepCycle: final / Resolution: 1.192→44.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 166 737 5761
Biso mean--24.01 32.24 -
Num. residues----645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085107
X-RAY DIFFRACTIONf_angle_d1.2796923
X-RAY DIFFRACTIONf_chiral_restr0.078809
X-RAY DIFFRACTIONf_plane_restr0.006877
X-RAY DIFFRACTIONf_dihedral_angle_d14.4481941
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 (%)
1.192-1.22230.4658960.4312105011059763
1.2223-1.25530.36671130.3709128421295578
1.2553-1.29230.3041370.3158149971513490
1.2923-1.3340.30671480.2839162971644598
1.334-1.38170.25471480.2321164481659699
1.3817-1.4370.241490.2055164401658999
1.437-1.50240.24041490.1931165601670999
1.5024-1.58160.20111490.15531651516664100
1.5816-1.68070.18191500.14671661316763100
1.6807-1.81050.20971490.14611659116740100
1.8105-1.99270.19671490.1676163511650098
1.9927-2.2810.14451510.1401165661671799
2.281-2.87370.14461490.1387167261687599
2.8737-44.5560.1651540.1468170271718199

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