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- PDB-5nqb: Rabbit Muscle L-lactate dehydrogenase in complex with malonate -

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Basic information

Entry
Database: PDB / ID: 5nqb
TitleRabbit Muscle L-lactate dehydrogenase in complex with malonate
ComponentsL-lactate dehydrogenase A chain
KeywordsOXIDOREDUCTASE / malonate
Function / homology
Function and homology information


L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / cytoplasm
Similarity search - Function
L-lactate dehydrogenase active site. / L-lactate dehydrogenase / 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 active site. / L-lactate dehydrogenase / 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 / 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
MALONATE ION / L-lactate dehydrogenase A chain
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsLuisi, B.F. / Olin-Sandoval, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust094229/Z/10/Z United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization.
Authors: Alam, M.T. / Olin-Sandoval, V. / Stincone, A. / Keller, M.A. / Zelezniak, A. / Luisi, B.F. / Ralser, M.
History
DepositionApr 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: 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 A chain
B: L-lactate dehydrogenase A chain
C: L-lactate dehydrogenase A chain
D: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,10911
Polymers146,3944
Non-polymers7147
Water25,3291406
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23430 Å2
ΔGint-111 kcal/mol
Surface area45670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.806, 76.952, 118.858
Angle α, β, γ (deg.)90.00, 96.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
L-lactate dehydrogenase A chain / LDH-A / LDH muscle subunit / LDH-M


Mass: 36598.547 Da / Num. of mol.: 4 / Mutation: T248->S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: LDHA / Production host: Escherichia coli (E. coli) / References: UniProt: P13491, L-lactate dehydrogenase
#2: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1406 / 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: 2.2 Å3/Da / Density % sol: 44.01 %
Crystal growTemperature: 293 K
Details: crystals were cryoprotected by washing in reservoir supplemented with 20% w/v PEG400 and 2.5 mM oxaloacetate before freezing in liquid nitrogen.
Method: vapor diffusion, hanging drop
Details: The crystallisation condition is 10% w/v PEG3350 and 0.1 M sodium malonate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.58→29.423 Å / Num. obs: 318978 / % possible obs: 89.7 % / Redundancy: 2.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Net I/σ(I): 8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H3F

3h3f


Resolution: 1.58→29.423 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 25.42
RfactorNum. reflection% reflection
Rfree0.2178 15234 4.97 %
Rwork0.1927 --
obs0.194 155035 89.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.58→29.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10145 0 49 1406 11600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910408
X-RAY DIFFRACTIONf_angle_d1.0514096
X-RAY DIFFRACTIONf_dihedral_angle_d16.7646267
X-RAY DIFFRACTIONf_chiral_restr0.0661662
X-RAY DIFFRACTIONf_plane_restr0.0071772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5797-1.59760.39384460.35028092X-RAY DIFFRACTION76
1.5976-1.61640.35954440.32918735X-RAY DIFFRACTION80
1.6164-1.63610.34444440.33298967X-RAY DIFFRACTION82
1.6361-1.65680.34574460.32698889X-RAY DIFFRACTION82
1.6568-1.67860.32384960.32468864X-RAY DIFFRACTION82
1.6786-1.70160.35284700.31668991X-RAY DIFFRACTION84
1.7016-1.72590.31745710.316710141X-RAY DIFFRACTION93
1.7259-1.75170.32035260.302310052X-RAY DIFFRACTION94
1.7517-1.7790.35135120.310110009X-RAY DIFFRACTION93
1.779-1.80820.32095420.286110112X-RAY DIFFRACTION93
1.8082-1.83940.2945660.276310053X-RAY DIFFRACTION93
1.8394-1.87280.27494530.26569980X-RAY DIFFRACTION92
1.8728-1.90880.28835060.25899957X-RAY DIFFRACTION91
1.9088-1.94780.29765420.24049738X-RAY DIFFRACTION91
1.9478-1.99010.25964730.23619638X-RAY DIFFRACTION89
1.9901-2.03640.25985120.22089019X-RAY DIFFRACTION84
2.0364-2.08730.27094610.220610375X-RAY DIFFRACTION94
2.0873-2.14380.22445210.205310246X-RAY DIFFRACTION94
2.1438-2.20680.23065220.184610101X-RAY DIFFRACTION94
2.2068-2.2780.22924770.184410136X-RAY DIFFRACTION93
2.278-2.35940.21515470.17610038X-RAY DIFFRACTION93
2.3594-2.45380.21814900.17649997X-RAY DIFFRACTION93
2.4538-2.56550.19035580.16849741X-RAY DIFFRACTION90
2.5655-2.70060.20355400.179663X-RAY DIFFRACTION90
2.7006-2.86970.19795080.174310439X-RAY DIFFRACTION96
2.8697-3.0910.19615680.170210287X-RAY DIFFRACTION95
3.091-3.40170.17895140.158310024X-RAY DIFFRACTION93
3.4017-3.8930.15884880.14579376X-RAY DIFFRACTION87
3.893-4.90110.15145630.132310203X-RAY DIFFRACTION95
4.9011-29.42820.16755280.14959645X-RAY DIFFRACTION89

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