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

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Basic information

Entry
Database: PDB / ID: 6fkv
TitleStructure and function of aldehyde dehydrogenase from Thermus thermophilus: An enzyme with an evolutionarily-distinct C-terminal arm (Recombinant protein with shortened C-terminal, ADH508)
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / aldehyde dehydrogenase / Thermus thermophilus
Function / homology
Function and homology information


aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / nucleotide binding
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)116,33318
Polymers114,9622
Non-polymers1,37116
Water30617
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
hetero molecules

A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,66736
Polymers229,9254
Non-polymers2,74232
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area29700 Å2
ΔGint-298 kcal/mol
Surface area59440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.190, 105.190, 314.570
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: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 4 - 506 / Label seq-ID: 10 - 512

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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aldehyde dehydrogenase


Mass: 57481.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: TT_C0513 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72KD3, aldehyde dehydrogenase (NAD+)

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Non-polymers , 5 types, 33 molecules

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


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.88 Å3/Da / Density % sol: 68.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 50 mM MOPS pH 7.5, 1.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.23→99.7200568611 Å / Num. obs: 39303 / % possible obs: 86.76 % / Redundancy: 6.4 % / Biso Wilson estimate: 51.9054394987 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.13 / Rrim(I) all: 0.36 / Net I/σ(I): 4.41
Reflection shellResolution: 2.23→2.316 Å / Num. unique obs: 3904

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Processing

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

4wj9


Resolution: 2.9→48.04 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 15.451 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R: 0.692 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22864 2000 5.1 %RANDOM
Rwork0.18993 ---
obs0.19192 37301 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.192 Å2
Baniso -1Baniso -2Baniso -3
1-2.82 Å2-0 Å2-0 Å2
2--2.82 Å2-0 Å2
3----5.63 Å2
Refinement stepCycle: 1 / Resolution: 2.9→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7900 0 77 17 7994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0158167
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177310
X-RAY DIFFRACTIONr_angle_refined_deg1.521.76911081
X-RAY DIFFRACTIONr_angle_other_deg0.4991.71517094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20551007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40518.167360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.467151092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3331576
X-RAY DIFFRACTIONr_chiral_restr0.0650.21004
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219305
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021591
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_it3.6835.4524035
X-RAY DIFFRACTIONr_mcbond_other3.6835.4534035
X-RAY DIFFRACTIONr_mcangle_it5.5788.1765039
X-RAY DIFFRACTIONr_mcangle_other5.5788.1775040
X-RAY DIFFRACTIONr_scbond_it4.7275.9574131
X-RAY DIFFRACTIONr_scbond_other4.6765.9444107
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2248.726007
X-RAY DIFFRACTIONr_long_range_B_refined9.97334804
X-RAY DIFFRACTIONr_long_range_B_other9.9734800
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 16794 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 148 -
Rwork0.334 2742 -
obs--99.04 %

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