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- PDB-7dl0: The mutant E310G/A314Y of 3,5-DAHDHcca complex with NADPH -

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Basic information

Entry
Database: PDB / ID: 7dl0
TitleThe mutant E310G/A314Y of 3,5-DAHDHcca complex with NADPH
Components3,5-diaminohexanoate dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / complex / NADPH
Function / homology
Function and homology information


L-erythro-3,5-diaminohexanoate dehydrogenase / L-erythro-3,5-diaminohexanoate dehydrogenase activity / quinone reductase (NADPH) activity / mRNA 3'-UTR AU-rich region binding / NADPH binding / cytosol
Similarity search - Function
Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 3,5-diaminohexanoate dehydrogenase
Similarity search - Component
Biological speciesCloacimonas acidaminovorans
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.17 Å
AuthorsLiu, N. / Wu, L. / Zhu, D.M. / Zhou, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2177020792 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Crystal Structures and Catalytic Mechanism of l-erythro-3,5-Diaminohexanoate Dehydrogenase and Rational Engineering for Asymmetric Synthesis of beta-Amino Acids.
Authors: Liu, N. / Wu, L. / Feng, J. / Sheng, X. / Li, J. / Chen, X. / Li, J. / Liu, W. / Zhou, J. / Wu, Q. / Zhu, D.
History
DepositionNov 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3,5-diaminohexanoate dehydrogenase
B: 3,5-diaminohexanoate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,18716
Polymers78,3562
Non-polymers1,83114
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-60 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.882, 161.882, 125.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-508-

HOH

21B-585-

HOH

31B-606-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 3,5-diaminohexanoate dehydrogenase / 3 / 5-DAHDHcca


Mass: 39178.043 Da / Num. of mol.: 2 / Mutation: E310G/A314Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cloacimonas acidaminovorans (strain Evry) (bacteria)
Gene: kdd, CLOAM1348 / Production host: Escherichia coli DH1 (bacteria)
References: UniProt: B0VJ11, L-erythro-3,5-diaminohexanoate dehydrogenase

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Non-polymers , 8 types, 220 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgSO4, 14% w/v PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 44317 / % possible obs: 99.2 % / Redundancy: 0.27 % / Biso Wilson estimate: 35.4133354041 Å2 / Rmerge(I) obs: 0.27 / Net I/σ(I): 16.3
Reflection shellResolution: 2.17→2.21 Å / Rmerge(I) obs: 1.542 / Num. unique obs: 2029 / Rpim(I) all: 0.501

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data processing
HKL-3000data scaling
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.17→40.56 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 2010 5.13 %
Rwork0.2114 37198 -
obs0.2143 39208 89.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.85 Å2 / Biso mean: 50.394 Å2 / Biso min: 14.52 Å2
Refinement stepCycle: final / Resolution: 2.17→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5368 0 114 206 5688
Biso mean--48.37 40.71 -
Num. residues----705
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.17-2.230.7513260.756540342914
2.23-2.290.5633790.41841509158851
2.29-2.360.3081250.26622507263285
2.36-2.430.31481540.24812832298697
2.43-2.520.2871660.24729533119100
2.52-2.620.32971470.249129603107100
2.62-2.740.2931640.245729593123100
2.74-2.880.27321540.252329503104100
2.88-3.060.28831690.229729763145100
3.06-3.30.29311570.23129703127100
3.3-3.630.25851570.199329953152100
3.63-4.160.25161760.178329893165100
4.16-5.240.21441690.169430473216100
5.24-40.560.24941670.18623148331599

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