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- PDB-3d0o: Crystal structure of Lactate Dehydrogenase from Staphylococcus Aureus -

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Basic information

Entry
Database: PDB / ID: 3d0o
TitleCrystal structure of Lactate Dehydrogenase from Staphylococcus Aureus
ComponentsL-lactate dehydrogenase 1
KeywordsOXIDOREDUCTASE / lactate dehydrogenase / staphylococcus aureus / Cytoplasm / Glycolysis / NAD / Phosphoprotein
Function / homology
Function and homology information


L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / glycolytic 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
L-lactate dehydrogenase 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsHo, M. / Gutierrez, J.A. / Almo, S.C. / Schramm, V.L.
CitationJournal: To be Published
Title: Crystal structure of Lactate Dehydrogenase from Staphylococcus Aureus
Authors: Ho, M. / Gutierrez, J.A. / Almo, S.C. / Schramm, V.L.
History
DepositionMay 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 1
B: L-lactate dehydrogenase 1


Theoretical massNumber of molelcules
Total (without water)69,2432
Polymers69,2432
Non-polymers00
Water9,602533
1
A: L-lactate dehydrogenase 1
B: L-lactate dehydrogenase 1

A: L-lactate dehydrogenase 1
B: L-lactate dehydrogenase 1


Theoretical massNumber of molelcules
Total (without water)138,4854
Polymers138,4854
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area15270 Å2
ΔGint-68 kcal/mol
Surface area42550 Å2
MethodPISA
2
A: L-lactate dehydrogenase 1

A: L-lactate dehydrogenase 1


Theoretical massNumber of molelcules
Total (without water)69,2432
Polymers69,2432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4330 Å2
ΔGint-27 kcal/mol
Surface area24640 Å2
MethodPISA
3
B: L-lactate dehydrogenase 1

B: L-lactate dehydrogenase 1


Theoretical massNumber of molelcules
Total (without water)69,2432
Polymers69,2432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4310 Å2
ΔGint-26 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.765, 74.503, 96.306
Angle α, β, γ (deg.)90.00, 129.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 34621.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: ldh1, SACOL0222 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q5HJD7, L-lactate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.65 Å3/Da / Density % sol: 53.59 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorDate: Apr 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 75432 / % possible obs: 94.6 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.084 / Χ2: 0.8 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.761.60.25953510.52267.1
1.76-1.8320.26269800.56688.3
1.83-1.912.50.2577680.66597.9
1.91-2.022.90.19878490.76598.9
2.02-2.143.10.16278600.8498.8
2.14-2.313.10.12878810.9799.2
2.31-2.543.10.10379450.84699.4
2.54-2.913.10.08179290.77399.6
2.91-3.663.10.06779240.73499.1
3.66-503.10.0779450.9297.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.4.0069refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.37 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.13 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.203 3311 5 %RANDOM
Rwork0.17 ---
obs0.172 66144 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.897 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å2-0.44 Å2
2---0.07 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4842 0 0 533 5375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224937
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9656716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1775647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.37524.612219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87515863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7961531
X-RAY DIFFRACTIONr_chiral_restr0.1270.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213717
X-RAY DIFFRACTIONr_mcbond_it0.8671.53120
X-RAY DIFFRACTIONr_mcangle_it1.50825051
X-RAY DIFFRACTIONr_scbond_it2.76631817
X-RAY DIFFRACTIONr_scangle_it4.5214.51652
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 211 -
Rwork0.194 4472 -
all-4683 -
obs--94.36 %

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