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- PDB-6sci: Structure of AdhE form 1 -

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Basic information

Entry
Database: PDB / ID: 6sci
TitleStructure of AdhE form 1
ComponentsAldehyde-alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / aldehyde alcohol dehydrogenase
Function / homology
Function and homology information


ethanol biosynthetic process / mixed acid fermentation / alcohol dehydrogenase (NAD+) activity, iron-dependent / acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / carbon utilization / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / ferrous iron binding / protein homooligomerization ...ethanol biosynthetic process / mixed acid fermentation / alcohol dehydrogenase (NAD+) activity, iron-dependent / acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / carbon utilization / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / ferrous iron binding / protein homooligomerization / response to oxidative stress / membrane / identical protein binding / cytosol
Similarity search - Function
Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-type alcohol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-type alcohol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
: / Bifunctional aldehyde-alcohol dehydrogenase AdhE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsLovering, A.L. / Bragginton, E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: High-resolution structure of the alcohol dehydrogenase domain of the bifunctional bacterial enzyme AdhE.
Authors: Azmi, L. / Bragginton, E.C. / Cadby, I.T. / Byron, O. / Roe, A.J. / Lovering, A.L. / Gabrielsen, M.
History
DepositionJul 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 2.0Mar 17, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site.label_seq_id ..._atom_site.auth_seq_id / _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_end_seq_num / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Jan 24, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)99,9024
Polymers99,7902
Non-polymers1122
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-45 kcal/mol
Surface area29650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.030, 96.730, 122.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALA(chain 'A' and (resid 451 through 533 or resid 535...AA451 - 5323 - 84
12PHEPHEGLYGLY(chain 'A' and (resid 451 through 533 or resid 535...AA535 - 54587 - 97
13PROPROARGARG(chain 'A' and (resid 451 through 533 or resid 535...AA548 - 579100 - 131
14LYSLYSALAALA(chain 'A' and (resid 451 through 533 or resid 535...AA582 - 753134 - 305
15GLNGLNLYSLYS(chain 'A' and (resid 451 through 533 or resid 535...AA770 - 831322 - 383
16GLUGLUVALVAL(chain 'A' and (resid 451 through 533 or resid 535...AA834 - 868386 - 420
27METMETALAALA(chain 'B' and (resid 451 through 487 or (resid 488...BB451 - 5323 - 84
28PHEPHEGLYGLY(chain 'B' and (resid 451 through 487 or (resid 488...BB535 - 54587 - 97
29PROPROARGARG(chain 'B' and (resid 451 through 487 or (resid 488...BB548 - 579100 - 131
210LYSLYSALAALA(chain 'B' and (resid 451 through 487 or (resid 488...BB582 - 753134 - 305
211GLNGLNLYSLYS(chain 'B' and (resid 451 through 487 or (resid 488...BB770 - 831322 - 383
212GLUGLUVALVAL(chain 'B' and (resid 451 through 487 or (resid 488...BB834 - 868386 - 420

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Components

#1: Protein Aldehyde-alcohol dehydrogenase


Mass: 49895.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: adhE, ana, b1241, JW1228 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A9Q7, alcohol dehydrogenase, acetaldehyde dehydrogenase (acetylating)
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Na Hepes pH 7.0 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97957 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.95→76.01 Å / Num. obs: 62248 / % possible obs: 99.7 % / Redundancy: 4.4 % / Biso Wilson estimate: 24.95 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.052 / Rrim(I) all: 0.111 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-24.50.6722062645820.7180.3480.762.399.8
8.72-57.253.80.05229267770.9940.030.0626.796.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.3.11data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SCR

6scr


Resolution: 1.95→57.25 Å / SU ML: 0.1834 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.6332
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 3028 4.87 %RANDOM
Rwork0.1825 59154 --
obs0.1842 62182 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.86 Å2
Refinement stepCycle: LAST / Resolution: 1.95→57.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6206 0 2 125 6333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00786359
X-RAY DIFFRACTIONf_angle_d1.03128626
X-RAY DIFFRACTIONf_chiral_restr0.0571980
X-RAY DIFFRACTIONf_plane_restr0.00621112
X-RAY DIFFRACTIONf_dihedral_angle_d8.2882876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.2571410.23752673X-RAY DIFFRACTION99.72
1.98-2.010.31381180.23812661X-RAY DIFFRACTION99.86
2.01-2.050.26141410.22792656X-RAY DIFFRACTION99.86
2.05-2.080.26461490.22022661X-RAY DIFFRACTION99.68
2.08-2.120.26321250.20092647X-RAY DIFFRACTION99.78
2.13-2.170.2461650.19482617X-RAY DIFFRACTION99.71
2.17-2.220.2391400.19062670X-RAY DIFFRACTION99.65
2.22-2.270.24691250.1942674X-RAY DIFFRACTION99.47
2.27-2.320.22471270.17872691X-RAY DIFFRACTION99.75
2.32-2.390.20051360.17962639X-RAY DIFFRACTION99.75
2.39-2.460.22891420.1752703X-RAY DIFFRACTION99.79
2.46-2.540.21231470.18152642X-RAY DIFFRACTION99.54
2.54-2.630.21091710.18432641X-RAY DIFFRACTION99.75
2.63-2.730.2511360.18882700X-RAY DIFFRACTION99.75
2.73-2.860.20061290.18832697X-RAY DIFFRACTION99.61
2.86-3.010.20341380.19662684X-RAY DIFFRACTION99.86
3.01-3.20.24241340.20952688X-RAY DIFFRACTION99.68
3.2-3.440.25491440.20192712X-RAY DIFFRACTION99.65
3.44-3.790.2251170.19142717X-RAY DIFFRACTION99.54
3.79-4.340.1821250.14792745X-RAY DIFFRACTION99.38
4.34-5.460.15141360.14632783X-RAY DIFFRACTION99.45
5.46-57.250.19511420.16362853X-RAY DIFFRACTION98.16
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)
10.932418678105-0.41647461736-0.125802398742.361888630560.4295945830260.928896848338-0.0134282904723-0.111485582079-0.09658213627250.4870541705690.07764724718660.007648822673990.2171272508190.0283088595804-0.04727987547620.248390982591-0.000316288929422-0.03303523505520.1232036019630.008634792049730.168015017541-33.072144028912.4402292116-13.253030174
21.375366212380.0453579261851-0.06874888568372.16036680449-0.01276075200040.892675027228-0.008294743640640.15842493270.165931971422-0.356723465079-0.02722788924790.132983469885-0.201898240415-0.06645981484410.01161269836690.2317811595950.032581031695-0.03635081244450.1389308152470.0285606980850.165762088687-45.154636817910.6316734795-45.1402517621
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 451:869)A451 - 869
2X-RAY DIFFRACTION2(chain B and resseq 451:869)B451 - 869

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