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- PDB-6k13: Crystal Structure Basis for BmLDH Complex -

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Basic information

Entry
Database: PDB / ID: 6k13
TitleCrystal Structure Basis for BmLDH Complex
ComponentsL-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / Babesia microti lactate dehydrogenase / Glycolysis / Lactate dehydrogenase
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / OXAMIC ACID / L-lactate dehydrogenase
Similarity search - Component
Biological speciesBabesia microti
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsLong, Y. / Shen, Z.
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

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Assembly

Deposited unit
A: L-lactate dehydrogenase
B: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9666
Polymers73,4612
Non-polymers1,5054
Water2,558142
1
A: L-lactate dehydrogenase
B: L-lactate dehydrogenase
hetero molecules

A: L-lactate dehydrogenase
B: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,93212
Polymers146,9224
Non-polymers3,0108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area28590 Å2
ΔGint-171 kcal/mol
Surface area40830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.400, 88.204, 92.631
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-569-

HOH

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Components

#1: Protein L-lactate dehydrogenase


Mass: 36730.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Babesia microti (strain RI) (eukaryote)
Strain: RI / Gene: BMR1_01G00020 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): BL21 / References: UniProt: I7J7V6, L-lactate dehydrogenase
#2: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H3NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / References: L-lactate dehydrogenase / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium Chloride, 0.1 M Imidazole, HCl pH 8.0, 1.6 M K2HPO4

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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: ADSC QUANTUM 315 / Detector: CCD / 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: 1.8→46.3294 Å / Num. obs: 53697 / % possible obs: 99.35 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.9
Reflection shellResolution: 1.8→1.9229 Å / Rmerge(I) obs: 0.025 / Num. unique obs: 53755

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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: 4ZVV

4zvv


Resolution: 1.89→44.102 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2128 2729 5.08 %
Rwork0.1802 50967 -
obs0.1818 53696 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.37 Å2 / Biso mean: 33.8836 Å2 / Biso min: 13.2 Å2
Refinement stepCycle: final / Resolution: 1.89→44.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5059 0 156 142 5357
Biso mean--25.79 27.43 -
Num. residues----655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055242
X-RAY DIFFRACTIONf_angle_d0.7727101
X-RAY DIFFRACTIONf_chiral_restr0.049844
X-RAY DIFFRACTIONf_plane_restr0.004888
X-RAY DIFFRACTIONf_dihedral_angle_d15.7393162
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8903-1.92470.3563122250094
1.9247-1.96170.29171402661100
1.9617-2.00180.23841082687100
2.0018-2.04530.26471242699100
2.0453-2.09290.2558146264999
2.0929-2.14520.26141482656100
2.1452-2.20320.24831552685100
2.2032-2.2680.2548164260499
2.268-2.34120.22621482661100
2.3412-2.42490.25241502667100
2.4249-2.5220.26481682658100
2.522-2.63670.23461622669100
2.6367-2.77570.2451412692100
2.7757-2.94960.21321512695100
2.9496-3.17730.22571602689100
3.1773-3.49690.25041012743100
3.4969-4.00260.1742125273499
4.0026-5.04170.14171740.1328271099
5.04170.16861420.14172908100

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