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- PDB-3pqd: Crystal structure of L-lactate dehydrogenase from Bacillus subtil... -

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Basic information

Entry
Database: PDB / ID: 3pqd
TitleCrystal structure of L-lactate dehydrogenase from Bacillus subtilis complexed with FBP and NAD+
ComponentsL-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / Lactate dehydrogenase / FBP / NAD+
Function / homology
Function and homology information


L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate 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
1,6-di-O-phosphono-beta-D-fructofuranose / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-lactate dehydrogenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.376 Å
AuthorsZhang, Y. / Garavito, R.M.
CitationJournal: To be Published
Title: Crystal structure of L-lactate dehydrogenase from Bacillus subtilis complexed with FBP and NAD+
Authors: zhang, Y. / Garavito, R.M.
History
DepositionNov 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
B: L-lactate dehydrogenase
C: L-lactate dehydrogenase
D: L-lactate dehydrogenase
E: L-lactate dehydrogenase
F: L-lactate dehydrogenase
G: L-lactate dehydrogenase
H: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,38713
Polymers285,3638
Non-polymers2,0245
Water2,594144
1
A: L-lactate dehydrogenase
B: L-lactate dehydrogenase
C: L-lactate dehydrogenase
D: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,0257
Polymers142,6824
Non-polymers1,3443
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16360 Å2
ΔGint-93 kcal/mol
Surface area43760 Å2
MethodPISA
2
E: L-lactate dehydrogenase
F: L-lactate dehydrogenase
G: L-lactate dehydrogenase
H: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,3626
Polymers142,6824
Non-polymers6802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15750 Å2
ΔGint-86 kcal/mol
Surface area43030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.041, 171.041, 96.272
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 35670.402 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ldh, lctE, BSU03050 / Plasmid: pLW01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P13714, L-lactate dehydrogenase
#2: Sugar
ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEGmme 2K, 0.1M Na/K PO4,pH 5.5, 1mM NAD+, 1mM FBP , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.376→29.445 Å / Num. all: 126217 / Num. obs: 126217 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.376→29.445 Å / SU ML: 0.36 / σ(F): 1.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 3816 3.02 %random
Rwork0.2139 ---
all0.2155 126217 --
obs0.2155 126217 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.582 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.095 Å2-0 Å20 Å2
2---0.095 Å20 Å2
3---0.1901 Å2
Refinement stepCycle: LAST / Resolution: 2.376→29.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18737 0 124 144 19005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00619222
X-RAY DIFFRACTIONf_angle_d1.126083
X-RAY DIFFRACTIONf_dihedral_angle_d24.34411688
X-RAY DIFFRACTIONf_chiral_restr0.0732974
X-RAY DIFFRACTIONf_plane_restr0.0043345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3765-2.40660.25221040.1824272X-RAY DIFFRACTION91
2.4066-2.43820.25981380.18774382X-RAY DIFFRACTION98
2.4382-2.47160.26711320.18754542X-RAY DIFFRACTION99
2.4716-2.50690.27751490.20234563X-RAY DIFFRACTION100
2.5069-2.54430.27511560.21174520X-RAY DIFFRACTION100
2.5443-2.5840.28431590.22584560X-RAY DIFFRACTION100
2.584-2.62640.31891400.22864509X-RAY DIFFRACTION100
2.6264-2.67160.29231300.21694613X-RAY DIFFRACTION100
2.6716-2.72020.26861370.22324524X-RAY DIFFRACTION100
2.7202-2.77240.2961440.25174554X-RAY DIFFRACTION100
2.7724-2.8290.32021430.25424578X-RAY DIFFRACTION100
2.829-2.89040.34811580.2584540X-RAY DIFFRACTION100
2.8904-2.95760.35891480.24614497X-RAY DIFFRACTION100
2.9576-3.03150.32381180.25064633X-RAY DIFFRACTION100
3.0315-3.11340.32931130.24884605X-RAY DIFFRACTION100
3.1134-3.20490.32041310.24654509X-RAY DIFFRACTION100
3.2049-3.30820.2781370.23834537X-RAY DIFFRACTION100
3.3082-3.42630.29351420.23884598X-RAY DIFFRACTION100
3.4263-3.56320.28051690.21884543X-RAY DIFFRACTION100
3.5632-3.72510.2561500.21174532X-RAY DIFFRACTION100
3.7251-3.92110.2361600.214524X-RAY DIFFRACTION100
3.9211-4.16610.25531550.24549X-RAY DIFFRACTION100
4.1661-4.48680.25141410.17854552X-RAY DIFFRACTION100
4.4868-4.93640.21981400.18344537X-RAY DIFFRACTION100
4.9364-5.64630.2381460.20014575X-RAY DIFFRACTION100
5.6463-7.09730.2631400.20474548X-RAY DIFFRACTION100
7.0973-29.44770.21781360.17344505X-RAY DIFFRACTION99

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