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- PDB-5dru: Structure of His387Ala mutant of the propionaldehyde dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 5dru
TitleStructure of His387Ala mutant of the propionaldehyde dehydrogenase from the Clostridium phytofermentans fucose utilisation bacterial microcompartment
ComponentsAldehyde Dehydrogenase
KeywordsOXIDOREDUCTASE / Acylating aldehyde dehydrogenase / bacterial microcompartment
Function / homology
Function and homology information


acetaldehyde dehydrogenase (acetylating) activity / nucleotide binding
Similarity search - Function
Acetaldehyde/propionaldehyde dehydrogenase, EutE/PduP-related / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase ...Acetaldehyde/propionaldehyde dehydrogenase, EutE/PduP-related / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aldehyde Dehydrogenase
Similarity search - Component
Biological speciesClostridium phytofermentans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.083 Å
AuthorsTuck, L.R. / Altenbach, K. / Fu, A.T. / Crawshaw, A.D. / Campopiano, D.J. / Clarke, D.J. / Marles-Wright, J.
CitationJournal: Sci Rep / Year: 2016
Title: Insight into Coenzyme A cofactor binding and the mechanism of acyl-transfer in an acylating aldehyde dehydrogenase from Clostridium phytofermentans.
Authors: Tuck, L.R. / Altenbach, K. / Ang, T.F. / Crawshaw, A.D. / Campopiano, D.J. / Clarke, D.J. / Marles-Wright, J.
History
DepositionSep 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Aldehyde Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7262
Polymers47,6301
Non-polymers961
Water2,270126
1
A: Aldehyde Dehydrogenase
hetero molecules

A: Aldehyde Dehydrogenase
hetero molecules

A: Aldehyde Dehydrogenase
hetero molecules

A: Aldehyde Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,9038
Polymers190,5194
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area16060 Å2
ΔGint-65 kcal/mol
Surface area56660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.448, 138.448, 84.758
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Aldehyde Dehydrogenase /


Mass: 47629.781 Da / Num. of mol.: 1 / Fragment: UNP residues 20-462 / Mutation: H387A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium phytofermentans (bacteria) / Gene: Cphy_1178 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9KN57
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.42 % / Description: bipyramidal
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: PROTEIN IN 50 MM TRIS.HCL, PH 8.0, 150 MM NACL. 1:2 HANGING DROPS OVER: 0.1 M SODIUM ACETATE, PH 4.7, 1.7 - 1.8 M AMMONIUM SULPHATE
PH range: 4.5 - 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2015
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.083→40.53 Å / Num. all: 24570 / Num. obs: 24570 / % possible obs: 98.85 % / Redundancy: 10 % / Rmerge(I) obs: 0.081 / Rsym value: 0.085 / Net I/σ(I): 18.94
Reflection shellResolution: 2.083→2.158 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.227 / Mean I/σ(I) obs: 1.63 / % possible all: 99.25

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4c3s

4c3s


Resolution: 2.083→40.53 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 1259 5.18 %Random selection
Rwork0.1823 ---
obs0.1862 24318 97.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.083→40.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3245 0 5 126 3376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153294
X-RAY DIFFRACTIONf_angle_d1.4424457
X-RAY DIFFRACTIONf_dihedral_angle_d14.5271227
X-RAY DIFFRACTIONf_chiral_restr0.057530
X-RAY DIFFRACTIONf_plane_restr0.008578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0833-2.16670.3111500.26042547X-RAY DIFFRACTION99
2.1667-2.26530.48351190.36412329X-RAY DIFFRACTION91
2.2653-2.38470.34081580.24782576X-RAY DIFFRACTION100
2.3847-2.53410.30671360.22372590X-RAY DIFFRACTION100
2.5341-2.72970.32151420.21922583X-RAY DIFFRACTION100
2.7297-3.00440.29721400.20772586X-RAY DIFFRACTION99
3.0044-3.43890.2631390.19472603X-RAY DIFFRACTION99
3.4389-4.33190.21061350.14922601X-RAY DIFFRACTION98
4.3319-40.53850.20651400.13812644X-RAY DIFFRACTION95
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)
13.69821.9345-0.35552.426-0.3991.18170.4386-0.40030.20180.6155-0.28440.0973-0.41320.1188-0.15480.6705-0.06610.08540.4845-0.06680.3513-11.893616.273723.983
24.39634.9159-2.51536.3644-4.1333.42330.2698-0.383-0.74410.7753-0.3369-0.343-0.543-0.13540.23230.34990.0104-0.04040.35830.07660.3008-12.20593.042319.2824
36.40031.4659-4.69762.0076-1.09424.23520.0156-0.0801-0.2510.1497-0.09-0.0358-0.15950.0213-0.02610.38950.0429-0.02480.3350.0030.2742-4.380513.49043.7056
43.01991.0329-0.46532.5863-0.28032.02440.5205-0.19740.26710.3464-0.34950.3011-0.5704-0.1205-0.1260.5675-0.02070.10850.2784-0.02480.3225-16.577419.625119.6411
52.9654-0.1168-0.66511.01830.06081.782-0.09460.0908-0.3250.19850.00630.23610.1461-0.50940.12350.3335-0.01680.06920.45650.01390.3752-33.4665-5.277612.4232
66.7566-3.9893-0.58676.67111.53426.30250.0388-0.1637-0.13670.6884-0.20650.5324-0.4395-0.75280.00040.57170.08710.15570.71610.00440.3973-41.61920.370424.0042
71.71480.2981-0.87911.1048-0.24431.3648-0.07560.2389-0.08810.07960.10650.17230.0027-0.4368-0.01730.36470.01410.0130.45510.03860.3444-23.2482-1.41944.4731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 110 )
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 138 )
4X-RAY DIFFRACTION4chain 'A' and (resid 139 through 218 )
5X-RAY DIFFRACTION5chain 'A' and (resid 219 through 310 )
6X-RAY DIFFRACTION6chain 'A' and (resid 311 through 341 )
7X-RAY DIFFRACTION7chain 'A' and (resid 342 through 462 )

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