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- PDB-8hr6: leucine DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ from... -

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Basic information

Entry
Database: PDB / ID: 8hr6
Titleleucine DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ from Bacillus thuringiensis
ComponentsLeucine dehydrogenase
KeywordsOXIDOREDUCTASE / leucine DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ from Bacillus thuringiensis
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE / :
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.52 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 14, 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)82,11515
Polymers79,7322
Non-polymers2,38413
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-157 kcal/mol
Surface area30630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.434, 121.434, 178.472
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, EC: 1.4.1.9
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% glycerol, 3.75% isopropanol, 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 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Mar 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.52→30.79 Å / Num. obs: 17215 / % possible obs: 99.8 % / Redundancy: 12.6 % / CC1/2: 0.995 / Net I/σ(I): 7.8
Reflection shellResolution: 3.52→3.85 Å / Num. unique obs: 4016 / CC1/2: 0.948

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5refinement
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.52→30.79 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.875 / SU B: 63.832 / SU ML: 0.434 / Cross valid method: THROUGHOUT / ESU R Free: 0.587 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27867 860 5 %RANDOM
Rwork0.22953 ---
obs0.232 16295 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.61 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å2-0 Å2-0 Å2
2--1.39 Å20 Å2
3----2.78 Å2
Refinement stepCycle: 1 / Resolution: 3.52→30.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5470 0 143 3 5616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0135691
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155343
X-RAY DIFFRACTIONr_angle_refined_deg1.381.6437719
X-RAY DIFFRACTIONr_angle_other_deg1.1241.58412293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0195710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1522.784291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.75215951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4311536
X-RAY DIFFRACTIONr_chiral_restr0.0490.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021229
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_it1.7034.8292854
X-RAY DIFFRACTIONr_mcbond_other1.7034.8292853
X-RAY DIFFRACTIONr_mcangle_it3.0147.2363559
X-RAY DIFFRACTIONr_mcangle_other3.0147.2373560
X-RAY DIFFRACTIONr_scbond_it1.4255.2822836
X-RAY DIFFRACTIONr_scbond_other1.3735.1522793
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5357.6884094
X-RAY DIFFRACTIONr_long_range_B_refined8.27858.0556176
X-RAY DIFFRACTIONr_long_range_B_other8.19958.0536175
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10851 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.53→3.608 Å
RfactorNum. reflection% reflection
Rfree0.43 64 -
Rwork0.319 1164 -
obs--98.48 %
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)
12.06750.06220.43661.34020.15250.7683-0.01160.1073-0.2348-0.0342-0.007-0.09620.09580.00440.01870.40650.05510.02950.3138-0.03750.27139.866231.194738.2522
20.148-0.1964-0.66110.28651.0424.12320.03390.15650.00920.0282-0.15510.02710.1978-0.24330.12120.32910.08330.16870.4384-0.07290.247722.48831.945212.1118
37.83991.5594-2.69516.3314-0.27874.3324-0.0043-0.42560.0135-0.0237-0.1065-0.59290.5614-0.04390.11080.2730.12250.06880.3806-0.06510.157634.296325.844823.7631
41.3012-0.9542-1.72670.70161.28412.47890.0126-0.0815-0.032-0.03390.06730.0154-0.25060.2041-0.07990.41550.04270.05640.35030.00260.326424.690945.176230.8438
51.8908-1.3281-0.0771.8488-0.49550.3368-0.2096-0.1368-0.18070.17480.16480.0159-0.0117-0.02310.04480.41820.02780.00910.37390.07470.25787.013531.470362.5529
61.37972.81850.12655.7860.17030.52620.2143-0.1471-0.170.5654-0.2137-0.321-0.3544-0.0422-0.00060.61030.39210.10150.52630.19680.0847-4.173126.849589.2157
72.46920.18911.33380.10190.0470.83930.2612-0.14850.2626-0.0019-0.23510.0470.29930.0438-0.02610.49330.0611-0.10240.5916-0.02390.38725.637223.835393.7163
87.45640.11624.50214.5806-1.11623.0389-1.10740.088-1.34780.38651.91910.2276-0.7524-0.3854-0.81170.26850.27580.34131.02050.30710.4689-2.52513.690781.2392
92.67541.488-0.80587.7705-0.8510.3339-0.6286-0.2239-0.04390.00360.76510.00190.0913-0.0768-0.13650.34780.07090.10150.41430.26840.3163-9.397731.830274.021
101.4354-0.87281.46730.7744-1.26462.16490.076-0.4325-0.0724-0.42170.24820.10150.5709-0.4078-0.32420.6332-0.0350.04270.34030.09290.3239-12.660233.527258.8197
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 131
2X-RAY DIFFRACTION2A132 - 263
3X-RAY DIFFRACTION3A264 - 284
4X-RAY DIFFRACTION4A285 - 365
5X-RAY DIFFRACTION5B3 - 168
6X-RAY DIFFRACTION6B169 - 197
7X-RAY DIFFRACTION7B198 - 218
8X-RAY DIFFRACTION8B219 - 277
9X-RAY DIFFRACTION9B278 - 328
10X-RAY DIFFRACTION10B329 - 365

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