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- PDB-3zdr: Structure of the Alcohol dehydrogenase (ADH) domain of a bifuncti... -

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Basic information

Entry
Database: PDB / ID: 3zdr
TitleStructure of the Alcohol dehydrogenase (ADH) domain of a bifunctional ADHE dehydrogenase from Geobacillus thermoglucosidasius NCIMB 11955
ComponentsALCOHOL DEHYDROGENASE DOMAIN OF THE BIFUNCTIONAL ACETALDEHYDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / BIFUNCTIONAL ALCOHOL/ALDEHYDE DEHYDROGENASE / BIOETHANOL
Function / homology
Function and homology information


acetaldehyde dehydrogenase (acetylating) activity / alcohol metabolic process / carbon utilization / alcohol dehydrogenase (NAD+) activity / metal ion binding
Similarity search - Function
Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-type alcohol dehydrogenase-like / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-type alcohol dehydrogenase-like / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Aldehyde-alcohol dehydrogenase
Similarity search - Component
Biological speciesGEOBACILLUS THERMOGLUCOSIDASIUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.504 Å
AuthorsExtance, J. / Crennell, S.J. / Eley, K. / Cripps, R. / Hough, D.W. / Danson, M.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of a Bifunctional Alcohol Dehydrogenase Involved in Bioethanol Generation in Geobacillus Thermoglucosidasius
Authors: Extance, J. / Crennell, S.J. / Eley, K. / Cripps, R. / Hough, D.W. / Danson, M.J.
History
DepositionNov 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references / Structure summary
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALCOHOL DEHYDROGENASE DOMAIN OF THE BIFUNCTIONAL ACETALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9474
Polymers48,6931
Non-polymers2543
Water48627
1
A: ALCOHOL DEHYDROGENASE DOMAIN OF THE BIFUNCTIONAL ACETALDEHYDE DEHYDROGENASE
hetero molecules

A: ALCOHOL DEHYDROGENASE DOMAIN OF THE BIFUNCTIONAL ACETALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8938
Polymers97,3862
Non-polymers5076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4610 Å2
ΔGint-127.2 kcal/mol
Surface area31250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.721, 96.588, 58.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ALCOHOL DEHYDROGENASE DOMAIN OF THE BIFUNCTIONAL ACETALDEHYDE DEHYDROGENASE / ACETALDEHYDE DEHYDROGENASE (ACETYLATING) / ADHE BIFUNCTIONAL DEHYDROGENASE


Mass: 48693.152 Da / Num. of mol.: 1 / Fragment: RESIDUES 457-867
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL ADH DOMAIN, STARTING AT RESIDUE 459
Source: (gene. exp.) GEOBACILLUS THERMOGLUCOSIDASIUS (bacteria)
Strain: TM242
Description: THE NCIMB 11955 STRAIN ENGINEERED BY TMO RENEWABLES LTD TO INCREASE ETHANOL PRODUCTION.
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: F8CW95, acetaldehyde dehydrogenase (acetylating), alcohol dehydrogenase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsNON-PUBLISHED GENOME. THE PROTEIN COMES FROM A DIFFERENT STRAIN OF GEOBACILLUS, HENCE THE NUMBERING MISMATCH.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 5
Details: 0.1 M SODIUM ACETATE PH 5.0, 0.1 M AMMONIUM SULPHATE, 0.3 M SODIUM FORMATE, 11.5% (V/V) PEG2K MME, AND 3-3.5% (V/V) PGA-LM (30% GLYCEROL CRYOPROTECTANT)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 30, 2011 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→48.29 Å / Num. obs: 13897 / % possible obs: 93.5 % / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.7
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.1 / % possible all: 77

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RRM

1rrm


Resolution: 2.504→48.294 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 696 5 %
Rwork0.1744 --
obs0.1774 13863 93.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.24 Å2
Refinement stepCycle: LAST / Resolution: 2.504→48.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 0 12 27 3221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043291
X-RAY DIFFRACTIONf_angle_d0.7134465
X-RAY DIFFRACTIONf_dihedral_angle_d16.1231227
X-RAY DIFFRACTIONf_chiral_restr0.043492
X-RAY DIFFRACTIONf_plane_restr0.003570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5037-2.6970.31211190.21262307X-RAY DIFFRACTION83
2.697-2.96840.28951530.20272385X-RAY DIFFRACTION87
2.9684-3.39780.25621510.19392712X-RAY DIFFRACTION97
3.3978-4.28050.23011310.15962835X-RAY DIFFRACTION100
4.2805-48.3030.21181420.16542928X-RAY DIFFRACTION98

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