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- PDB-4c3s: Structure of a propionaldehyde dehydrogenase from the Clostridium... -

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Basic information

Entry
Database: PDB / ID: 4c3s
TitleStructure of a propionaldehyde dehydrogenase from the Clostridium phytofermentans fucose utilisation bacterial microcompartment
ComponentsALDEHYDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aldehyde Dehydrogenase
Similarity search - Component
Biological speciesCLOSTRIDIUM PHYTOFERMENTANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsMarles-Wright, J. / Crawshaw, A. / Ang, T.F. / Altenbach, K.
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
DepositionAug 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Atomic model / Other
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)48,8417
Polymers47,6971
Non-polymers1,1446
Water7,800433
1
A: ALDEHYDE DEHYDROGENASE
hetero molecules

A: ALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,68114
Polymers95,3942
Non-polymers2,28712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area8550 Å2
ΔGint-137.7 kcal/mol
Surface area31040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.488, 138.488, 84.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-2074-

HOH

21A-2124-

HOH

31A-2206-

HOH

41A-2207-

HOH

51A-2236-

HOH

61A-2240-

HOH

71A-2328-

HOH

81A-2412-

HOH

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Components

#1: Protein ALDEHYDE DEHYDROGENASE / PROPANAL DEHYDROGENASE


Mass: 47696.848 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PHYTOFERMENTANS (bacteria) / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A9KN57, acetaldehyde dehydrogenase (acetylating)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST 19 AMINO ACIDS TRUNCATED FROM CONSTRUCT CRYSTALLISED.

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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: 2.13 Å3/Da / Density % sol: 42.35 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.7
Details: PROTEIN IN 50 MM TRIS.HCL, PH 8.0, 35 MM NACL. 1:1 HANGING DROPS OVER: 0.1 M SODIUM ACETATE, PH 4.5 - 4.8 1.4 - 1.8 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 17, 2012 / Details: MIRRORS
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.64→32.64 Å / Num. obs: 50131 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.8
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1439)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K9D

3k9d


Resolution: 1.64→30.967 Å / SU ML: 0.13 / σ(F): 29.99 / Phase error: 15.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1738 2515 5 %
Rwork0.1463 --
obs0.1477 50118 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→30.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3250 0 69 433 3752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013416
X-RAY DIFFRACTIONf_angle_d1.354645
X-RAY DIFFRACTIONf_dihedral_angle_d15.2781284
X-RAY DIFFRACTIONf_chiral_restr0.052548
X-RAY DIFFRACTIONf_plane_restr0.007594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.67150.24681650.22232589X-RAY DIFFRACTION100
1.6715-1.70570.20861360.19682608X-RAY DIFFRACTION100
1.7057-1.74270.21791360.18932631X-RAY DIFFRACTION100
1.7427-1.78330.18371210.18362647X-RAY DIFFRACTION100
1.7833-1.82790.21911280.17382623X-RAY DIFFRACTION100
1.8279-1.87730.23031340.16622641X-RAY DIFFRACTION100
1.8773-1.93250.20621380.16082640X-RAY DIFFRACTION100
1.9325-1.99490.19131440.1542608X-RAY DIFFRACTION100
1.9949-2.06620.17771550.14722630X-RAY DIFFRACTION100
2.0662-2.14890.20191500.14242600X-RAY DIFFRACTION100
2.1489-2.24670.18281290.13222662X-RAY DIFFRACTION100
2.2467-2.36510.1381420.12832641X-RAY DIFFRACTION100
2.3651-2.51320.16181340.13572653X-RAY DIFFRACTION100
2.5132-2.70710.17581290.13882675X-RAY DIFFRACTION100
2.7071-2.97940.18831540.15032649X-RAY DIFFRACTION100
2.9794-3.410.18791390.14932666X-RAY DIFFRACTION99
3.41-4.29440.1281440.12092688X-RAY DIFFRACTION99
4.2944-30.97240.151370.14472752X-RAY DIFFRACTION97
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)
10.05160.00530.02350.3379-0.3020.28860.1724-0.21380.21920.3962-0.06210.2326-0.50110.1376-0.43460.5404-0.13580.1530.2401-0.07240.2288-10.339227.229420.2668
20.81040.2043-0.53850.3742-0.06160.66680.1473-0.3367-0.00290.1792-0.12290.0073-0.17440.168-0.04040.1753-0.02660.01920.20690.01940.1214-9.86538.714617.9102
30.34170.52240.03580.83310.20060.82740.2474-0.25250.30920.2743-0.24310.372-0.4021-0.0337-0.48260.2815-0.06670.14530.1396-0.02570.1219-16.50219.62819.6711
41.52660.3308-0.63991.169-0.21530.99760.02320.0497-0.07550.0834-0.0420.13-0.051-0.1182-0.00280.11710.01840.03230.15370.00340.1509-27.2602-0.189110.3918
50.20840.18570.19510.3976-0.05410.7344-0.0892-0.1145-0.38180.2355-0.05190.4408-0.0172-0.4439-0.71270.17410.01270.14250.29050.00470.3345-41.2962-6.34818.7398
61.1391-0.0008-0.20390.2635-0.32960.8437-0.01560.2106-0.19090.0406-0.05190.2044-0.0379-0.3107-0.04250.11550.00040.03080.2231-0.03190.2321-34.0948-6.58133.9989
71.46460.2703-0.53120.5406-0.24110.43180.026-0.0099-0.050.1068-0.02390.0024-0.0462-0.0287-0.00490.11220.00630.00460.09940.00860.0844-10.12984.87785.2239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 28 THROUGH 51 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 52 THROUGH 138 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 139 THROUGH 218 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 219 THROUGH 271 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 272 THROUGH 341 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 342 THROUGH 406 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 407 THROUGH 462 )

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