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- PDB-8ab2: Crystal Structure of the Lactate Dehydrogenase of Cyanobacterium ... -

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Basic information

Entry
Database: PDB / ID: 8ab2
TitleCrystal Structure of the Lactate Dehydrogenase of Cyanobacterium Aponinum in its apo form.
ComponentsL-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / allostery / lactate dehydrogenase / crystallophore / XO4
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / glycolytic 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
Tb-Xo4 / TERBIUM(III) ION / L-lactate dehydrogenase
Similarity search - Component
Biological speciesCyanobacterium aponinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsRobin, A.Y. / Girard, E. / Madern, D.
Funding support France, 2items
OrganizationGrant numberCountry
Other governmentprogram CrysFrag R&D booster region AuRA France
Other governmentProgram XO4_2.0 Pack ambition recherche region AuRA France
CitationJournal: Mol.Biol.Evol. / Year: 2023
Title: Deciphering Evolutionary Trajectories of Lactate Dehydrogenases Provides New Insights into Allostery.
Authors: Robin, A.Y. / Brochier-Armanet, C. / Bertrand, Q. / Barette, C. / Girard, E. / Madern, D.
History
DepositionJul 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)38,1316
Polymers37,0361
Non-polymers1,0955
Water3,405189
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)152,52424
Polymers148,1434
Non-polymers4,38120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area21260 Å2
ΔGint-216 kcal/mol
Surface area51870 Å2
Unit cell
Length a, b, c (Å)103.797, 103.797, 197.824
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein L-lactate dehydrogenase / L-LDH


Mass: 37035.699 Da / Num. of mol.: 1 / Mutation: Cter 6 histidine tag
Source method: isolated from a genetically manipulated source
Details: numbering in coordinates files start at 3 for the first residue (to match canonical numbering). two last residues and histag not defined in electronic density.
Source: (gene. exp.) Cyanobacterium aponinum (bacteria) / Strain: PCC 10605 / Gene: ldh, Cyan10605_1816 / Production host: Escherichia coli (E. coli) / References: UniProt: K9Z684, L-lactate dehydrogenase
#2: Chemical ChemComp-7MT / Tb-Xo4


Mass: 556.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N5O4Tb / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Tb
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 3.6 Å3/Da / Density % sol: 65.8 % / Description: bipyramid
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 21 % Peg MME 550, 0.1 M NaCl, 0.1 M bicine pH 9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.984 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.1→45.19 Å / Num. obs: 31611 / % possible obs: 98.98 % / Redundancy: 9.7 % / Biso Wilson estimate: 40.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.026 / Rsym value: 0.081 / Net I/σ(I): 19.35
Reflection shellResolution: 2.1→2.176 Å / Num. unique obs: 2966 / CC1/2: 0.913 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
SCALAdata scaling
CRANK2phasing
MxCuBEdata collection
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.1→37.96 Å / SU ML: 0.2618 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.8123
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2234 1580 5 %
Rwork0.183 30014 -
obs0.185 31594 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 37 189 2704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00182593
X-RAY DIFFRACTIONf_angle_d0.45193526
X-RAY DIFFRACTIONf_chiral_restr0.0437422
X-RAY DIFFRACTIONf_plane_restr0.0038451
X-RAY DIFFRACTIONf_dihedral_angle_d11.8209955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.36871340.28362544X-RAY DIFFRACTION93.93
2.17-2.250.30941410.23942690X-RAY DIFFRACTION98.85
2.25-2.340.28791410.24042656X-RAY DIFFRACTION98.24
2.34-2.440.2821420.21942690X-RAY DIFFRACTION99.44
2.44-2.570.26611420.20972723X-RAY DIFFRACTION99.48
2.57-2.730.27031440.21312731X-RAY DIFFRACTION99.76
2.73-2.940.26271440.22822739X-RAY DIFFRACTION99.76
2.94-3.240.25061450.20872736X-RAY DIFFRACTION99.86
3.24-3.710.23521450.18712764X-RAY DIFFRACTION99.97
3.71-4.670.19451480.1412804X-RAY DIFFRACTION100
4.67-37.960.15661540.14792937X-RAY DIFFRACTION99.74
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.05644622043040.1798149702980.04711017310040.121790569965-0.1177298616280.05154354116150.03552006100470.035296855542-0.0926991221570.0006983881389590.0659905315771-0.1326465745620.2130596585140.03710752699150.008290641324990.325879490070.080283147794-0.01884894564360.3629012506860.04301152759870.35185071781668.560952054-9.675228832763.6600867047
20.152846664527-0.2405696155470.008994361390450.0793593310040.0760086664390.4285228306680.0433724487341-0.08139674836480.04413751158250.05637438305360.07122999349880.0299073871078-0.06035620929740.3267108595350.001008135927030.234363372507-0.009269089490920.002466569423770.397591044876-0.03562054732120.31188196224678.62264626735.6833238725444.4631500148
3-0.04710374216790.03845811421530.3335107923720.2806927499530.008434802639160.47031807291-0.02236821889180.04522094108550.0121554108113-0.1393764792670.078354338362-0.01715877751-0.07914835702770.2061231176283.59121980703E-60.320320110407-0.0121673911580.02218261666290.313119671653-0.00459806747320.29367249140564.76891977767.7113258500225.1949602254
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 31 )3 - 311 - 29
22chain 'A' and (resid 32 through 153 )32 - 15330 - 151
33chain 'A' and (resid 154 through 330 )154 - 330152 - 328

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