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- PDB-5o8h: Crystal structure of R. ruber ADH-A, mutant Y294F, W295A, F43H, H39Y -

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Basic information

Entry
Database: PDB / ID: 5o8h
TitleCrystal structure of R. ruber ADH-A, mutant Y294F, W295A, F43H, H39Y
ComponentsAlcohol dehydrogenase
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase mutant variant / NADH-dependent / Zn2+-dependent / Rossmann fold
Function / homology
Function and homology information


oxidoreductase activity / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase
Similarity search - Component
Biological speciesRhodococcus sp. M8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsDobritzsch, D. / Maurer, D. / Hamnevik, E. / Reddy Enugala, T. / Widersten, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: FEBS J. / Year: 2017
Title: Relaxation of nonproductive binding and increased rate of coenzyme release in an alcohol dehydrogenase increases turnover with a nonpreferred alcohol enantiomer.
Authors: Hamnevik, E. / Enugala, T.R. / Maurer, D. / Ntuku, S. / Oliveira, A. / Dobritzsch, D. / Widersten, M.
History
DepositionJun 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: Alcohol dehydrogenase
B: Alcohol dehydrogenase
C: Alcohol dehydrogenase
D: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,28719
Polymers143,9404
Non-polymers3,34715
Water20,2131122
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15760 Å2
ΔGint-251 kcal/mol
Surface area45220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.702, 105.678, 109.623
Angle α, β, γ (deg.)90.00, 91.51, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA1 - 3461 - 346
21THRTHRBB1 - 3461 - 346
12THRTHRAA1 - 3461 - 346
22THRTHRCC1 - 3461 - 346
13VALVALAA1 - 3441 - 344
23VALVALDD1 - 3441 - 344
14THRTHRBB1 - 3461 - 346
24THRTHRCC1 - 3461 - 346
15VALVALBB1 - 3441 - 344
25VALVALDD1 - 3441 - 344
16VALVALCC1 - 3441 - 344
26VALVALDD1 - 3441 - 344

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Alcohol dehydrogenase /


Mass: 35984.887 Da / Num. of mol.: 4 / Mutation: Y294F, W295A, F43H, H39Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. M8 (bacteria) / Gene: BKE56_025765 / Plasmid: pGT7ADHA-5H / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: A0A1Q8I6M1

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Non-polymers , 5 types, 1137 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 1122 / 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: 2.42 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 19% PAA5100, 0.1 M Tris pH 8, 4 mM NAD+, 20 mM MgCl2, 150 mM NaCl, 7.5 mg/ml ADH-A

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.96→29.63 Å / Num. obs: 107618 / % possible obs: 99.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.065 / Net I/σ(I): 6.9
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5020 / CC1/2: 0.574 / Rpim(I) all: 0.489 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3jv7
Resolution: 1.96→29.63 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.067 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20352 5190 4.8 %RANDOM
Rwork0.17563 ---
obs0.177 102015 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.466 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20.21 Å2
2--1 Å20 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.96→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9877 0 192 1122 11191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910334
X-RAY DIFFRACTIONr_bond_other_d0.0020.029731
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.98914145
X-RAY DIFFRACTIONr_angle_other_deg0.942322410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7451395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.59122.687361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.103151441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3951575
X-RAY DIFFRACTIONr_chiral_restr0.0770.21664
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022073
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_it1.8593.1385550
X-RAY DIFFRACTIONr_mcbond_other1.8593.1385549
X-RAY DIFFRACTIONr_mcangle_it2.744.6956937
X-RAY DIFFRACTIONr_mcangle_other2.744.6966938
X-RAY DIFFRACTIONr_scbond_it2.2633.3874784
X-RAY DIFFRACTIONr_scbond_other2.2633.3874784
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5194.9867203
X-RAY DIFFRACTIONr_long_range_B_refined5.68638.57311328
X-RAY DIFFRACTIONr_long_range_B_other5.68738.57711329
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A205620.03
12B205620.03
21A205120.03
22C205120.03
31A202240.04
32D202240.04
41B205700.03
42C205700.03
51B202400.05
52D202400.05
61C201420.05
62D201420.05
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 367 -
Rwork0.272 7511 -
obs--99.87 %

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