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- PDB-6fjx: Structure and function of aldehyde dehydrogenase from Thermus the... -

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Basic information

Entry
Database: PDB / ID: 6fjx
TitleStructure and function of aldehyde dehydrogenase from Thermus thermophilus: An enzyme with an evolutionarily-distinct C-terminal arm (Native protein)
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / aldehyde dehydrogenase / Thermus thermophilus
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / nucleotide binding
Similarity search - Function
Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHayes, K.A. / Noor, M.R. / Djeghader, A. / Soulimane, T.
CitationJournal: Sci Rep / Year: 2018
Title: The quaternary structure of Thermus thermophilus aldehyde dehydrogenase is stabilized by an evolutionary distinct C-terminal arm extension.
Authors: Hayes, K. / Noor, M. / Djeghader, A. / Armshaw, P. / Pembroke, T. / Tofail, S. / Soulimane, T.
History
DepositionJan 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 2.0Dec 19, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / struct_conn ...atom_site / struct_conn / struct_site / struct_site_gen
Item: _atom_site.label_alt_id
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)118,55611
Polymers117,2452
Non-polymers1,3119
Water5,260292
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
hetero molecules

A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,11322
Polymers234,4904
Non-polymers2,62318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area36080 Å2
ΔGint-281 kcal/mol
Surface area60610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.290, 105.290, 314.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 529 / Label seq-ID: 1 - 529

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Aldehyde dehydrogenase


Mass: 58622.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: Q72KD3, aldehyde dehydrogenase (NAD+)
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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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: 3.72 Å3/Da / Density % sol: 66.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 50 mM MOPS pH 7.5 and 1.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.25→48.08 Å / Num. obs: 84880 / % possible obs: 99.97 % / Redundancy: 30.3 % / Biso Wilson estimate: 41.3327863925 Å2 / CC1/2: 0.985 / Rpim(I) all: 0.09949 / Rrim(I) all: 0.5602 / Net I/σ(I): 12.1
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 26.6 % / Mean I/σ(I) obs: 2.21 / Num. unique obs: 8384 / % possible all: 99.99

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WJ9

4wj9


Resolution: 2.25→48.04 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.576 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20951 2000 2.4 %RANDOM
Rwork0.18856 ---
obs0.18905 82881 99.98 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.588 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å2-0 Å2-0 Å2
2--1.78 Å2-0 Å2
3----3.56 Å2
Refinement stepCycle: 1 / Resolution: 2.25→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8272 0 80 292 8644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0158571
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177677
X-RAY DIFFRACTIONr_angle_refined_deg0.8361.77411642
X-RAY DIFFRACTIONr_angle_other_deg0.2931.71617975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93351060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.78418.226372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.743151154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.681578
X-RAY DIFFRACTIONr_chiral_restr0.0360.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219742
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021658
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_it2.2124.2274234
X-RAY DIFFRACTIONr_mcbond_other2.2114.2284235
X-RAY DIFFRACTIONr_mcangle_it3.2276.3445290
X-RAY DIFFRACTIONr_mcangle_other3.2286.3445290
X-RAY DIFFRACTIONr_scbond_it3.4444.7394337
X-RAY DIFFRACTIONr_scbond_other3.4234.7274313
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.46.9086315
X-RAY DIFFRACTIONr_long_range_B_refined6.31451.3639629
X-RAY DIFFRACTIONr_long_range_B_other6.24651.1629517
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17997 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 145 -
Rwork0.315 6031 -
obs--100 %

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