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- PDB-8hpe: Crystal structure of Leucine dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 8hpe
TitleCrystal structure of Leucine dehydrogenase
ComponentsLeucine dehydrogenase
KeywordsOXIDOREDUCTASE / Leucine dehydrogenase
Function / homology:
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsLi, X. / Song, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chembiochem / Year: 2023
Title: A Tri-Enzyme Cascade for Efficient Production of L-2-Aminobutyrate from L-Threonine.
Authors: Li, X. / Gao, C. / Wei, W. / Song, W. / Meng, W. / Liu, J. / Chen, X. / Gao, C. / Guo, L. / Liu, L. / Wu, J.
History
DepositionDec 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,16517
Polymers79,7322
Non-polymers1,43315
Water18010
1
A: Leucine dehydrogenase
B: Leucine dehydrogenase
hetero molecules

A: Leucine dehydrogenase
B: Leucine dehydrogenase
hetero molecules

A: Leucine dehydrogenase
B: Leucine dehydrogenase
hetero molecules

A: Leucine dehydrogenase
B: Leucine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,65968
Polymers318,9278
Non-polymers5,73260
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area41860 Å2
ΔGint-762 kcal/mol
Surface area103590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.949, 120.949, 177.624
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Leucine dehydrogenase / Leucine dehydrogenase Ldh


Mass: 39865.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria)
Gene: ldh1, BK774_17255, BK775_32270, BTGOE4_46100, BUM91_06765, C5676_00473, D7J84_18335, GH851_02505, GH891_02550
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G3E5D9, leucine dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.07 Å3/Da / Density % sol: 69.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% glycerol, 1.5M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54184 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Dec 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 3.22→46.2 Å / Num. obs: 22022 / % possible obs: 99.9 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.302 / Net I/σ(I): 8.7
Reflection shellResolution: 3.22→3.48 Å / Rmerge(I) obs: 1.2 / Num. unique obs: 4448

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.22→46.24 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.869 / SU B: 61.788 / SU ML: 0.441 / Cross valid method: THROUGHOUT / ESU R Free: 0.499 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29529 1078 4.9 %RANDOM
Rwork0.23255 ---
obs0.23571 20926 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.592 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0 Å2
2--0.13 Å20 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 3.22→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5472 0 77 10 5559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135615
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175322
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.6397598
X-RAY DIFFRACTIONr_angle_other_deg1.1911.58312238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0895710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32422.784291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.81315952
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0591536
X-RAY DIFFRACTIONr_chiral_restr0.0570.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026363
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021213
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1473.3452854
X-RAY DIFFRACTIONr_mcbond_other1.1453.3452853
X-RAY DIFFRACTIONr_mcangle_it2.0295.0113559
X-RAY DIFFRACTIONr_mcangle_other2.0295.0123560
X-RAY DIFFRACTIONr_scbond_it1.1713.6342758
X-RAY DIFFRACTIONr_scbond_other1.1713.6352759
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9885.4214039
X-RAY DIFFRACTIONr_long_range_B_refined6.96339.6886140
X-RAY DIFFRACTIONr_long_range_B_other6.96339.6996141
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11051 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.221→3.305 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 71 -
Rwork0.34 1506 -
obs--98.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.90253.308-0.1064.87650.05760.45330.04210.3785-0.968-0.065-0.0454-0.47810.47460.19210.00340.56350.131-0.02030.3688-0.08330.160911.261429.572138.9378
25.0399-0.2454-0.86576.0343.55372.19780.0230.93850.1724-0.90360.016-0.0321-0.5133-0.1094-0.0390.44380.06170.06160.48490.06870.01874.168138.718632.5137
32.7241-0.6104-0.77143.6341.06756.0310.02530.3014-0.31220.0365-0.1258-0.11780.3259-0.04380.10050.45610.080.11050.5133-0.0490.118924.913631.489914.224
40.1192-0.5703-0.82574.25633.17826.22920.0007-0.00020.008-0.3030.0257-0.0948-0.03010.1551-0.02640.3814-0.04740.05120.52630.03320.127526.995245.606731.9759
56.9360.48530.50261.4723-0.6170.48470.1146-0.2344-0.58810.1643-0.1117-0.1160.22880.0813-0.00290.57760.0624-0.00610.34420.05680.05699.189731.630759.4605
64.4884-1.85642.23247.90240.75643.1994-0.7332-0.91270.26741.30560.84220.3583-0.5129-0.0244-0.10911.04150.37730.16670.98610.23460.2718-6.150127.825186.2017
70.6068-0.40951.17730.2901-0.79092.2954-0.5367-0.16780.24010.33930.1054-0.2766-0.9861-0.25380.43131.14590.207-0.04861.1314-0.01771.0575.806223.924493.1365
85.9332-1.50222.46198.7138-1.80195.5719-0.2714-0.4461-1.20830.09550.7440.50780.244-0.3061-0.47260.47690.15470.24970.64210.3340.5448-3.372513.873880.4856
97.88422.6439-2.32829.1448-2.24553.2565-0.4571-0.18940.46650.09110.67230.8857-0.2853-0.1381-0.21520.57210.12660.04670.58980.21270.269-9.130734.047173.0588
104.1472-5.64982.82077.7936-4.25126.1715-0.1384-0.331-0.19220.05670.42170.17870.3062-0.3001-0.28330.3492-0.07270.11320.38770.05140.1903-12.785633.323158.5338
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 106
2X-RAY DIFFRACTION2A107 - 148
3X-RAY DIFFRACTION3A149 - 304
4X-RAY DIFFRACTION4A305 - 365
5X-RAY DIFFRACTION5B3 - 148
6X-RAY DIFFRACTION6B149 - 197
7X-RAY DIFFRACTION7B198 - 218
8X-RAY DIFFRACTION8B219 - 284
9X-RAY DIFFRACTION9B285 - 328
10X-RAY DIFFRACTION10B329 - 365

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