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- PDB-6k12: Babesia microti lactate dehydrogenase apo form (BmLDH) -

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Basic information

Entry
Database: PDB / ID: 6k12
TitleBabesia microti lactate dehydrogenase apo form (BmLDH)
ComponentsL-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / lactate dehydrogenase / inhibitor
Function / homology
Function and homology information


L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / nucleotide binding / cytoplasm
Similarity search - Function
L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / 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 ...L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 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
L-lactate dehydrogenase
Similarity search - Component
Biological speciesBabesia microti
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.794 Å
AuthorsLong, Y.
CitationJournal: Faseb J. / Year: 2019
Title: Crystal structures ofBabesia microtilactate dehydrogenase BmLDH reveal a critical role for Arg99 in catalysis.
Authors: Yu, L. / Shen, Z. / Liu, Q. / Zhan, X. / Luo, X. / An, X. / Sun, Y. / Li, M. / Wang, S. / Nie, Z. / Ao, Y. / Zhao, Y. / Peng, G. / Mamoun, C.B. / He, L. / Zhao, J.
History
DepositionMay 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-lactate dehydrogenase
B: L-lactate dehydrogenase
C: L-lactate dehydrogenase
D: L-lactate dehydrogenase
E: L-lactate dehydrogenase
F: L-lactate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)219,8616
Polymers219,8616
Non-polymers00
Water00
1
A: L-lactate dehydrogenase
F: L-lactate dehydrogenase

A: L-lactate dehydrogenase
F: L-lactate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)146,5744
Polymers146,5744
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area12560 Å2
ΔGint-80 kcal/mol
Surface area42970 Å2
MethodPISA
2
B: L-lactate dehydrogenase
C: L-lactate dehydrogenase
D: L-lactate dehydrogenase
E: L-lactate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)146,5744
Polymers146,5744
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11560 Å2
ΔGint-84 kcal/mol
Surface area40920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)255.604, 147.677, 65.266
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
L-lactate dehydrogenase


Mass: 36643.449 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Babesia microti (strain RI) (eukaryote)
Strain: RI / Gene: BMR1_01G00020 / Variant: PRA-99 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: I7J7V6, L-lactate dehydrogenase

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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: 2.8 Å3/Da / Density % sol: 60.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M sodium acetate trihydrate PH 7.0, 11 ~ 15% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97736 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97736 Å / Relative weight: 1
ReflectionResolution: 2.79387→48.886 Å / Num. obs: 59522 / % possible obs: 99.3687 % / Redundancy: 3.5 % / Rrim(I) all: 0.1 / Net I/σ(I): 2
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 59822 / Rrim(I) all: 0.1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZXC

5zxc
PDB Unreleased entry


Resolution: 2.794→45.655 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3079 3009 5.06 %
Rwork0.2796 56513 -
obs0.2811 59522 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.12 Å2 / Biso mean: 68.2613 Å2 / Biso min: 32.54 Å2
Refinement stepCycle: final / Resolution: 2.794→45.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12435 0 0 0 12435
Num. residues----1628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01912607
X-RAY DIFFRACTIONf_angle_d1.03117025
X-RAY DIFFRACTIONf_chiral_restr0.0532062
X-RAY DIFFRACTIONf_plane_restr0.0082117
X-RAY DIFFRACTIONf_dihedral_angle_d19.864616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeNum. reflection RworkRefine-IDRfactor Rfree error% reflection obs (%)
2.794-2.83970.40131562548X-RAY DIFFRACTION092
2.8397-2.88860.42391272653X-RAY DIFFRACTION0100
2.8886-2.94110.39121292744X-RAY DIFFRACTION0100
2.9411-2.99770.36081592663X-RAY DIFFRACTION0100
2.9977-3.05890.31751722635X-RAY DIFFRACTION0100
3.0589-3.12540.42261272763X-RAY DIFFRACTION0100
3.1254-3.19810.36981552614X-RAY DIFFRACTION0100
3.1981-3.2780.37161182787X-RAY DIFFRACTION0100
3.278-3.36660.34481332686X-RAY DIFFRACTION0100
3.3666-3.46560.37771092743X-RAY DIFFRACTION0100
3.4656-3.57750.3271452731X-RAY DIFFRACTION0100
3.5775-3.70530.33451322671X-RAY DIFFRACTION0100
3.7053-3.85360.3611482745X-RAY DIFFRACTION0100
3.8536-4.02880.27871352732X-RAY DIFFRACTION0100
4.0288-4.24110.32161272667X-RAY DIFFRACTION0100
4.2411-4.50660.28141732671X-RAY DIFFRACTION0100
4.5066-4.85420.25931692692X-RAY DIFFRACTION0100
4.8542-5.3420.29651412744X-RAY DIFFRACTION0100
5.342-6.11350.27921452727X-RAY DIFFRACTION0100
6.1135-7.69630.32941642706X-RAY DIFFRACTION0100
7.6963-8.4570.23261452591X-RAY DIFFRACTION094

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