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- PDB-7vid: The crystal structure of L-leucine dehydrogenase from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 7vid
TitleThe crystal structure of L-leucine dehydrogenase from Pseudomonas aeruginosa
ComponentsLeucine dehydrogenase
KeywordsOXIDOREDUCTASE / Pseudomonas aeruginosa / PA3418 / leucine dehydrogenase / branched chain amino acid
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor / amino acid metabolic process / nucleotide binding
Similarity search - Function
Glutamate/phenylalanine/leucine/valine dehydrogenase, bacterial/archaeal / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Leucine dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKim, S. / Kang, W. / Yang, J.K.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A6A1A10044154 Korea, Republic Of
National Research Foundation (NRF, Korea)2019R1F1A106326813 Korea, Republic Of
CitationJournal: Mol.Cells / Year: 2022
Title: The Crystal Structure of L-Leucine Dehydrogenase from Pseudomonas aeruginosa.
Authors: Kim, S. / Koh, S. / Kang, W. / Yang, J.K.
History
DepositionSep 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucine dehydrogenase
B: Leucine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1854
Polymers73,0012
Non-polymers1842
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-9 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.620, 90.180, 61.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Leucine dehydrogenase /


Mass: 36500.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: ldh, PA3418 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HYI7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12 % (w/v) polyethylene glycol 3,350, 0.1M sodium acetate trihydrate
PH range: 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→90.2 Å / Num. obs: 28028 / % possible obs: 99.8 % / Redundancy: 11.6 % / Biso Wilson estimate: 47.17 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.16 / Net I/σ(I): 13.4
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4015 / CC1/2: 0.714 / Rrim(I) all: 1.42

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
SCALAdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LEH

1leh


Resolution: 2.5→76.22 Å / SU ML: 0.3493 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.6254
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2486 1404 5.02 %
Rwork0.1956 26570 -
obs0.1983 27974 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.17 Å2
Refinement stepCycle: LAST / Resolution: 2.5→76.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4814 0 12 74 4900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764902
X-RAY DIFFRACTIONf_angle_d0.96846661
X-RAY DIFFRACTIONf_chiral_restr0.0526773
X-RAY DIFFRACTIONf_plane_restr0.0079888
X-RAY DIFFRACTIONf_dihedral_angle_d6.1564738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.590.38411180.30872622X-RAY DIFFRACTION99.67
2.59-2.690.31561240.26892616X-RAY DIFFRACTION99.64
2.69-2.820.29591330.23232619X-RAY DIFFRACTION99.1
2.82-2.960.31641450.24682604X-RAY DIFFRACTION99.82
2.96-3.150.30271520.2572615X-RAY DIFFRACTION99.71
3.15-3.390.28251340.222678X-RAY DIFFRACTION99.93
3.39-3.730.25751600.19112614X-RAY DIFFRACTION99.68
3.73-4.270.21141300.17212677X-RAY DIFFRACTION99.75
4.28-5.380.22751570.15422687X-RAY DIFFRACTION99.79
5.39-76.220.19391510.16362838X-RAY DIFFRACTION99.53

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