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- PDB-3vpx: Crystal structure of leucine dehydrogenase from a psychrophilic b... -

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Basic information

Entry
Database: PDB / ID: 3vpx
TitleCrystal structure of leucine dehydrogenase from a psychrophilic bacterium Sporosarcina psychrophila.
ComponentsLeucine dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / leucine dehydrogense / NAD/leucine binding
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 / Leucine Dehydrogenase, chain A, domain 1 / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / 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 ...Glutamate/phenylalanine/leucine/valine dehydrogenase, bacterial/archaeal / Leucine Dehydrogenase, chain A, domain 1 / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / 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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Leucine dehydrogenase
Similarity search - Component
Biological speciesSporosarcina psychrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsZhao, Y. / Wakamatsu, T. / Doi, K. / Sakuraba, H. / Ohshima, T.
CitationJournal: J.MOL.CATAL., B ENZYM. / Year: 2012
Title: A psychrophilic leucine dehydrogenase from Sporosarcina psychrophila: Purification, characterization, gene sequencing and crystal structure analysis
Authors: Zhao, Y. / Wakamatsu, T. / Doi, K. / Sakuraba, H. / Ohshima, T.
History
DepositionMar 14, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Leucine dehydrogenase
B: Leucine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)78,7722
Polymers78,7722
Non-polymers00
Water1,20767
1
A: Leucine dehydrogenase
B: Leucine dehydrogenase

A: Leucine dehydrogenase
B: Leucine dehydrogenase

A: Leucine dehydrogenase
B: Leucine dehydrogenase

A: Leucine dehydrogenase
B: Leucine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)315,0908
Polymers315,0908
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area25080 Å2
ΔGint-68 kcal/mol
Surface area107690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.589, 135.589, 123.553
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Leucine dehydrogenase / / LeuDH


Mass: 39386.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sporosarcina psychrophila (bacteria) / Strain: DSM 3 / References: UniProt: I0IJU1, EC: 1.4.1.9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.6 Å3/Da / Density % sol: 65.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.05M trisodium citrate dehydrate, 0.05M lithium sulfate, 0.75M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 2, 2011
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 35953 / Num. obs: 35953 / % possible obs: 99.2 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 49.3
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 7.5 / Num. unique all: 1812 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LEH

1leh


Resolution: 2.55→31.78 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 3177 -RANDOM
Rwork0.243 ---
all-31963 --
obs-31963 87.7 %-
Displacement parametersBiso mean: 53.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.39 Å20 Å20 Å2
2---4.39 Å20 Å2
3---8.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.55→31.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5450 0 0 67 5517
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.372 471 -
Rwork0.305 --
obs-4073 75.2 %

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