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- PDB-7wn9: Dictyostelium discoideum Lactate dehydrogenase (DicLDHA) -

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Basic information

Entry
Database: PDB / ID: 7wn9
TitleDictyostelium discoideum Lactate dehydrogenase (DicLDHA)
ComponentsPutative D-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / lactate dehydrogenase
Function / homology
Function and homology information


D-lactate dehydrogenase / D-lactate dehydrogenase activity / phagocytic vesicle / NAD binding
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / Putative D-lactate dehydrogenase
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsDao, O. / Lee, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Dictyostelium discoideum Lactate dehydrogenase (DicLDHA)
Authors: Dao, O. / Lee, K.H.
History
DepositionJan 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 2.0Jul 12, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / software / struct_asym / struct_conf / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim
Item: _entity.pdbx_number_of_molecules / _pdbx_poly_seq_scheme.auth_mon_id ..._entity.pdbx_number_of_molecules / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _software.classification / _software.name / _software.version
Description: Sequence discrepancy / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative D-lactate dehydrogenase
B: Putative D-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,29513
Polymers76,6452
Non-polymers64911
Water13,061725
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-37 kcal/mol
Surface area27040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.344, 156.344, 183.739
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Putative D-lactate dehydrogenase / D-LDH


Mass: 38322.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: ldhA, DDB_G0281101 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q54UF7, D-lactate dehydrogenase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.67 Å3/Da / Density % sol: 66.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 1.9M Ammonium sulfate, 90 mM sodium acetate pH4.6

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 50412 / % possible obs: 100 % / Redundancy: 24.5 % / Rrim(I) all: 0.141 / Net I/σ(I): 5.6
Reflection shellResolution: 2.29→2.36 Å / Num. unique obs: 4234 / Rrim(I) all: 0.511

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOLREPphasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z1Z

5z1z


Resolution: 2.3→43.536 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 2611 5.18 %
Rwork0.1609 --
obs0.1628 50410 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→43.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5292 0 44 725 6061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075517
X-RAY DIFFRACTIONf_angle_d0.7557471
X-RAY DIFFRACTIONf_dihedral_angle_d11.9713366
X-RAY DIFFRACTIONf_chiral_restr0.054854
X-RAY DIFFRACTIONf_plane_restr0.004959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.34190.25571520.19132462X-RAY DIFFRACTION100
2.3419-2.3870.23611300.18842499X-RAY DIFFRACTION100
2.387-2.43570.21761430.17532517X-RAY DIFFRACTION100
2.4357-2.48860.22761430.18012463X-RAY DIFFRACTION100
2.4886-2.54650.24861310.17542478X-RAY DIFFRACTION100
2.5465-2.61020.24251560.1762516X-RAY DIFFRACTION100
2.6102-2.68080.19161280.16762470X-RAY DIFFRACTION100
2.6808-2.75960.21771480.16832489X-RAY DIFFRACTION100
2.7596-2.84870.20451220.1712511X-RAY DIFFRACTION100
2.8487-2.95050.23611310.17412520X-RAY DIFFRACTION100
2.9505-3.06860.20631150.17242543X-RAY DIFFRACTION100
3.0686-3.20820.2211360.16712504X-RAY DIFFRACTION100
3.2082-3.37730.21031320.15522525X-RAY DIFFRACTION100
3.3773-3.58880.20761500.15272512X-RAY DIFFRACTION100
3.5888-3.86570.16211380.13692525X-RAY DIFFRACTION100
3.8657-4.25450.16361510.1332548X-RAY DIFFRACTION100
4.2545-4.86940.16941430.12712552X-RAY DIFFRACTION100
4.8694-6.13220.20851290.16852597X-RAY DIFFRACTION100
6.1322-43.50.16691330.192568X-RAY DIFFRACTION94

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