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- PDB-3d4p: Crystal structure of Lactate Dehydrogenase from Staphylococcus Au... -

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Basic information

Entry
Database: PDB / ID: 3d4p
TitleCrystal structure of Lactate Dehydrogenase from Staphylococcus Aureus complexed with NAD and pyruvate
ComponentsL-lactate dehydrogenase 1
KeywordsOXIDOREDUCTASE / Lactate Dehydrogenase / Staphylococcus Aureus / NAD / pyruvate / Cytoplasm / Glycolysis / Phosphoprotein
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PYRUVIC ACID / L-lactate dehydrogenase 1
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsSchramm, V.L. / Almo, S.C. / Gutierrez, J.A. / Ho, M.
CitationJournal: To be Published
Title: Crystal structure of Lactate Dehydrogenase from Staphylococcus Aureus complexed with NAD and pyruvate
Authors: Schramm, V.L. / Almo, S.C. / Gutierrez, J.A. / Ho, M.
History
DepositionMay 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7466
Polymers69,2432
Non-polymers1,5034
Water5,495305
1
A: L-lactate dehydrogenase 1
B: L-lactate dehydrogenase 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)141,49112
Polymers138,4854
Non-polymers3,0068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area21640 Å2
ΔGint-77 kcal/mol
Surface area40650 Å2
MethodPISA
2
A: L-lactate dehydrogenase 1
hetero molecules

A: L-lactate dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7466
Polymers69,2432
Non-polymers1,5034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area7490 Å2
ΔGint-30 kcal/mol
Surface area23650 Å2
MethodPISA
3
B: L-lactate dehydrogenase 1
hetero molecules

B: L-lactate dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7466
Polymers69,2432
Non-polymers1,5034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area7540 Å2
ΔGint-31 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.868, 74.916, 95.874
Angle α, β, γ (deg.)90.000, 128.900, 90.000
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 subsp. aureus COL (bacteria)
Gene: ldh1, SACOL0222 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HJD7, L-lactate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 35% 2-methyl-2,4-pentanediol, 0.1M acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 66324 / % possible obs: 98.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.097 / Χ2: 0.729 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.862.90.24961440.48591.7
1.86-1.943.60.21165790.51598
1.94-2.034.10.16465850.58498.9
2.03-2.134.20.14366470.68699.1
2.13-2.274.20.11566740.77299.3
2.27-2.444.20.166700.86499.5
2.44-2.694.20.09467050.8599.7
2.69-3.084.20.08967140.81699.9
3.08-3.884.10.08167470.836100
3.88-504.10.08468590.72599.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0069refinement
PDB_EXTRACT3.005data extraction
RefinementResolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.796 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.188 3361 5.1 %RANDOM
Rwork0.163 ---
obs0.164 66322 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.765 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0.84 Å2
2--0.21 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4811 0 100 305 5216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225001
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9896816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1155640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.65724.769216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54115851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4041529
X-RAY DIFFRACTIONr_chiral_restr0.1150.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213735
X-RAY DIFFRACTIONr_mcbond_it0.8381.53101
X-RAY DIFFRACTIONr_mcangle_it1.54725019
X-RAY DIFFRACTIONr_scbond_it2.67431900
X-RAY DIFFRACTIONr_scangle_it4.4774.51785
LS refinement shellResolution: 1.8→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 200 -
Rwork0.193 4138 -
all-4338 -
obs--87.14 %

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