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- PDB-9dq9: Borrelia burgdorferi LDH with NADH and oxamate -

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Basic information

Entry
Database: PDB / ID: 9dq9
TitleBorrelia burgdorferi LDH with NADH and oxamate
ComponentsL-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / lactate dehydrogenase / oxamate / NADH
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / glycolytic process / cytosol
Similarity search - Function
L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / 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 domain superfamily
Similarity search - Domain/homology
Chem-6V0 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / OXAMIC ACID / L-lactate dehydrogenase
Similarity search - Component
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLynch, M.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01AI148844 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI078958 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DE023080 United States
CitationJournal: To Be Published
Title: Borrelia burgdorferi LDH with NADH and oxamate
Authors: Lynch, M.J.
History
DepositionSep 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)141,65017
Polymers138,4364
Non-polymers3,21413
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21130 Å2
ΔGint-152 kcal/mol
Surface area40950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.528, 90.348, 167.361
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules PABC

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


Mass: 34608.891 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Gene: ldh, BB_0087 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O51114, L-lactate dehydrogenase

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Non-polymers , 5 types, 163 molecules

#2: Chemical ChemComp-6V0 / [[(2~{R},3~{S},4~{R},5~{R})-5-(5-aminocarbonyl-2~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate / 6DHNAD


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical
ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 44.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES pH 7.4-7.6 100 mM calcium acetate 40% PEG400
PH range: 7.4-7.8

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.1→47.47 Å / Num. obs: 71544 / % possible obs: 97.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 42.83 Å2 / CC1/2: 0.799 / Rmerge(I) obs: 0.361 / Rpim(I) all: 0.154 / Rrim(I) all: 0.393 / Net I/σ(I): 3.7
Reflection shellResolution: 2.1→2.18 Å / Num. unique obs: 7019 / CC1/2: 0.405 / % possible all: 85.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.47 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 2000 2.84 %
Rwork0.2003 --
obs0.2011 70522 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9728 0 205 150 10083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310124
X-RAY DIFFRACTIONf_angle_d0.58613705
X-RAY DIFFRACTIONf_dihedral_angle_d7.9231365
X-RAY DIFFRACTIONf_chiral_restr0.0451598
X-RAY DIFFRACTIONf_plane_restr0.0051703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.36561190.35414065X-RAY DIFFRACTION83
2.15-2.210.34691370.33714706X-RAY DIFFRACTION95
2.21-2.280.35451410.32184834X-RAY DIFFRACTION98
2.28-2.350.32221420.30834878X-RAY DIFFRACTION99
2.35-2.430.32961440.28394933X-RAY DIFFRACTION99
2.43-2.530.29141440.25964903X-RAY DIFFRACTION99
2.53-2.650.29271430.24434920X-RAY DIFFRACTION99
2.65-2.790.27531440.23594934X-RAY DIFFRACTION100
2.79-2.960.29591450.23494961X-RAY DIFFRACTION99
2.96-3.190.23991450.21954986X-RAY DIFFRACTION100
3.19-3.510.23611470.195001X-RAY DIFFRACTION100
3.51-4.020.18671470.16755030X-RAY DIFFRACTION100
4.02-5.060.18881480.14035088X-RAY DIFFRACTION100
5.06-47.470.16971540.1665283X-RAY DIFFRACTION100

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