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- PDB-5nqq: Rabbit Muscle L-lactate dehydrogenase in complex with NADH and ox... -

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Basic information

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


L-lactate dehydrogenase / L-lactate dehydrogenase activity / lactate metabolic process / pyruvate metabolic process / 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 / 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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / OXALOACETATE ION / L-lactate dehydrogenase A chain
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.872 Å
AuthorsLuisi, B.F. / Olin-Sandoval, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust 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 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 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)149,70214
Polymers146,3944
Non-polymers3,30810
Water13,529751
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27900 Å2
ΔGint-244 kcal/mol
Surface area42490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.373, 138.763, 74.567
Angle α, β, γ (deg.)90.00, 110.12, 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: THR 248 TO SER
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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% wt/v PEG 3350, 50 mM Bis-tris propane pH 6.5 and 100 mM NaF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.872→29.42 Å / Num. obs: 220343 / % possible obs: 98.9 % / Redundancy: 6.6 % / Net I/σ(I): 14

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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: 1.872→29.416 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 22.07
RfactorNum. reflection% reflectionSelection details
Rfree0.199 11040 5.01 %Random selection
Rwork0.17 ---
obs0.1715 112037 98.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.872→29.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10163 0 214 751 11128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210610
X-RAY DIFFRACTIONf_angle_d1.22714396
X-RAY DIFFRACTIONf_dihedral_angle_d18.2296328
X-RAY DIFFRACTIONf_chiral_restr0.0671688
X-RAY DIFFRACTIONf_plane_restr0.0071775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8724-1.89360.37712860.38154722X-RAY DIFFRACTION67
1.8936-1.91590.34413510.31237116X-RAY DIFFRACTION99
1.9159-1.93930.34913290.30557001X-RAY DIFFRACTION99
1.9393-1.96380.32233660.29117083X-RAY DIFFRACTION99
1.9638-1.98970.27843830.26426881X-RAY DIFFRACTION98
1.9897-2.01690.25163330.26657084X-RAY DIFFRACTION99
2.0169-2.04570.29263650.25626985X-RAY DIFFRACTION99
2.0457-2.07620.26023860.24537035X-RAY DIFFRACTION99
2.0762-2.10870.27143060.22817081X-RAY DIFFRACTION99
2.1087-2.14320.24453770.20886973X-RAY DIFFRACTION99
2.1432-2.18020.223860.20177054X-RAY DIFFRACTION99
2.1802-2.21980.23523730.1937088X-RAY DIFFRACTION100
2.2198-2.26250.2323390.17437153X-RAY DIFFRACTION100
2.2625-2.30870.22254470.16556989X-RAY DIFFRACTION100
2.3087-2.35880.19384430.15797077X-RAY DIFFRACTION100
2.3588-2.41370.21083850.15557107X-RAY DIFFRACTION100
2.4137-2.4740.19393400.16157100X-RAY DIFFRACTION100
2.474-2.54090.19493890.15247058X-RAY DIFFRACTION100
2.5409-2.61560.17853140.15387180X-RAY DIFFRACTION100
2.6156-2.70.20373550.15427070X-RAY DIFFRACTION100
2.7-2.79640.19034460.15327110X-RAY DIFFRACTION100
2.7964-2.90830.20653450.16057089X-RAY DIFFRACTION100
2.9083-3.04050.20724340.16026956X-RAY DIFFRACTION100
3.0405-3.20060.17373780.16237099X-RAY DIFFRACTION100
3.2006-3.40090.19823350.15697174X-RAY DIFFRACTION100
3.4009-3.6630.18423930.15676988X-RAY DIFFRACTION99
3.663-4.03080.18063560.14417053X-RAY DIFFRACTION99
4.0308-4.61210.15443740.13096955X-RAY DIFFRACTION98
4.6121-5.80340.14793360.13797063X-RAY DIFFRACTION99
5.8034-29.41920.16743900.15956979X-RAY DIFFRACTION99

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