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- PDB-3h3j: Crystal structure of lactate dehydrogenase mutant (A85R) from sta... -

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Basic information

Entry
Database: PDB / ID: 3h3j
TitleCrystal structure of lactate dehydrogenase mutant (A85R) from staphylococcus aureus complexed with NAD and pyruvate
ComponentsL-lactate dehydrogenase 1
KeywordsOXIDOREDUCTASE / Rossmann Fold / alpha-beta motif / Cytoplasm / Glycolysis / NAD / Phosphoprotein / Stress response
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PYRUVIC ACID / L-lactate dehydrogenase 1
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHo, M.-C. / Almo, S.C. / Schramm, V.L.
CitationJournal: To be Published
Title: Crystal structure of lactate dehydrogenase mutant (A85R) from staphylococcus aureus complexed with NAD and pyruvate
Authors: Ho, M.-C. / Almo, S.C. / Schramm, V.L.
History
DepositionApr 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)71,1028
Polymers69,4152
Non-polymers1,6876
Water5,152286
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)142,20416
Polymers138,8304
Non-polymers3,37412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area22830 Å2
ΔGint-81 kcal/mol
Surface area38520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.917, 122.120, 74.319
Angle α, β, γ (deg.)90.000, 116.200, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-350-

HOH

21B-351-

HOH

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Components

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


Mass: 34707.477 Da / Num. of mol.: 2 / Mutation: A85R
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) / Strain (production host): BL21(DE3) / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG2000MME, 0.1M Tris buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.081 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.081 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 60471 / % possible obs: 98.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.078 / Χ2: 1.02 / Net I/σ(I): 16.693
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.8630.50653241.02987
1.86-1.943.30.41559101.03796.4
1.94-2.033.70.31661111.02299.7
2.03-2.133.90.25861411.074100
2.13-2.274.10.19561501.037100
2.27-2.444.20.14861301.027100
2.44-2.694.20.11161511.012100
2.69-3.074.20.07661871.012100
3.07-3.874.20.05461511.025100
3.87-204.10.03862160.9499.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3D4P

3d4p


Resolution: 1.8→19.7 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.953 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3065 5.1 %RANDOM
Rwork0.191 ---
obs0.194 57336 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.96 Å2 / Biso mean: 26.855 Å2 / Biso min: 14.43 Å2
Baniso -1Baniso -2Baniso -3
1--2.84 Å20 Å2-0.86 Å2
2--2.64 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4821 0 112 286 5219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225038
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9956844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2235631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.53524.771218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33515859
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9011530
X-RAY DIFFRACTIONr_chiral_restr0.0840.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213746
X-RAY DIFFRACTIONr_mcbond_it0.6261.53118
X-RAY DIFFRACTIONr_mcangle_it1.14825033
X-RAY DIFFRACTIONr_scbond_it1.97731920
X-RAY DIFFRACTIONr_scangle_it3.3094.51808
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 175 -
Rwork0.286 3602 -
all-3777 -
obs--82.81 %

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