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- PDB-6ffz: Crystal structure of R. ruber ADH-A, mutant F43H, Y54L -

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Basic information

Entry
Database: PDB / ID: 6ffz
TitleCrystal structure of R. ruber ADH-A, mutant F43H, Y54L
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 / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain ...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 / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / 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: 1.71 Å
AuthorsDobritzsch, D. / Maurer, D. / Hamnevik, E. / Enugala, T.R. / Widersten, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Biochemistry / Year: 2018
Title: Directed Evolution of Alcohol Dehydrogenase for Improved Stereoselective Redox Transformations of 1-Phenylethane-1,2-diol and Its Corresponding Acyloin.
Authors: Hamnevik, E. / Maurer, D. / Enugala, T.R. / Chu, T. / Lofgren, R. / Dobritzsch, D. / Widersten, M.
History
DepositionJan 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 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 / 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 / _struct_conn.pdbx_dist_value / _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_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)147,34116
Polymers144,1644
Non-polymers3,17712
Water26,0141444
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14900 Å2
ΔGint-254 kcal/mol
Surface area44630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.497, 105.572, 108.658
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: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

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

#1: Protein
Alcohol dehydrogenase


Mass: 36040.977 Da / Num. of mol.: 4 / Mutation: F43H, Y54L
Source method: isolated from a genetically manipulated source
Details: C-terminal His-tag / 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
#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


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1444 / 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: 2.32 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 15% Polyacrylic acid 5100 0.1 M Tris pH 8 4 mM NAD+ 20 mM MgCl2 7.5 mg/ml ADHA mutant

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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: 1.71→29.5 Å / Num. obs: 156099 / % possible obs: 98.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 20.4 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.056 / Rrim(I) all: 0.104 / Net I/σ(I): 6.3
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 2 % / Rmerge(I) obs: 0.657 / Num. unique obs: 5845 / CC1/2: 0.503 / Rpim(I) all: 0.542 / Rrim(I) all: 0.856 / % possible all: 74.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3jv7

3jv7


Resolution: 1.71→29.5 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.51 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.09 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18273 7867 5.1 %RANDOM
Rwork0.16139 ---
obs0.16246 147820 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.716 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0 Å20.38 Å2
2--0.31 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.71→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9893 0 184 1444 11521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910332
X-RAY DIFFRACTIONr_bond_other_d0.0020.029730
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.98814150
X-RAY DIFFRACTIONr_angle_other_deg0.938322413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78851393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.00722.833360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.727151446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.871573
X-RAY DIFFRACTIONr_chiral_restr0.0780.21668
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111746
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022055
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_it0.7631.7275545
X-RAY DIFFRACTIONr_mcbond_other0.7631.7275544
X-RAY DIFFRACTIONr_mcangle_it1.2842.5876929
X-RAY DIFFRACTIONr_mcangle_other1.2842.5876930
X-RAY DIFFRACTIONr_scbond_it0.9271.8324787
X-RAY DIFFRACTIONr_scbond_other0.9271.8324788
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5182.7027216
X-RAY DIFFRACTIONr_long_range_B_refined5.20723.15311809
X-RAY DIFFRACTIONr_long_range_B_other4.78121.57111250
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)
11A209760.03
12B209760.03
21A209700.04
22C209700.04
31A208240.03
32D208240.03
41B210640.05
42C210640.05
51B208740.04
52D208740.04
61C208120.05
62D208120.05
LS refinement shellResolution: 1.712→1.756 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 511 -
Rwork0.282 8851 -
obs--80.28 %
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)
10.80450.2150.06080.88250.09881.16760.0102-0.01530.10410.0596-0.0031-0.0612-0.16050.0796-0.00710.0392-0.0194-0.00660.0112-0.00070.023892.195615.3307139.1488
20.7688-0.0969-0.08480.83120.13171.0405-0.01620.0194-0.1549-0.0617-0.0051-0.0540.12920.04420.02130.03590.00360.01210.0032-0.00320.038189.4428-25.8732132.1993
31.0971-0.08870.14960.6825-0.02660.59530.0370.3219-0.0053-0.1703-0.04480.1119-0.0159-0.07640.00790.0620.0102-0.02780.14070.00310.025963.95990.1859114.2035
41.1404-0.06320.03041.0518-0.4740.8093-0.0495-0.361-0.00540.33390.08390.2172-0.1048-0.2164-0.03440.1150.01670.06390.17760.00710.071561.3791-6.3071154.1661
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 503
2X-RAY DIFFRACTION2B1 - 503
3X-RAY DIFFRACTION3C1 - 503
4X-RAY DIFFRACTION4D1 - 503

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