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- PDB-5od3: Crystal structure of R. ruber ADH-A, mutant Y54G, L119Y -

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Basic information

Entry
Database: PDB / ID: 5od3
TitleCrystal structure of R. ruber ADH-A, mutant Y54G, L119Y
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: 1.83 Å
AuthorsDobritzsch, D. / Maurer, D. / Hamnevik, E. / Enugala, T.R. / Widersten, M.
CitationJournal: Acs Catalysis / Year: 2018
Title: Stereo- and Regioselectivity in Catalyzed Transformation of a 1,2-Disubstituted Vicinal Diol and the Corresponding Diketone by Wild Type and Laboratory Evolved Alcohol Dehydrogenases
Authors: Maurer, D. / Enugala, T.R. / Hamnevik, E. / Bauer, P. / Luking, M. / Petrovic, D. / Hillier, H. / Kamerlin, S.C.L. / Dobritzsch, D. / Widersten, M.
History
DepositionJul 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
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)147,35316
Polymers144,1764
Non-polymers3,17712
Water21,2221178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15000 Å2
ΔGint-252 kcal/mol
Surface area44350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.555, 105.969, 108.076
Angle α, β, γ (deg.)90.00, 91.37, 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
11VALVALAA1 - 3441 - 344
21VALVALBB1 - 3441 - 344
12VALVALAA1 - 3441 - 344
22VALVALCC1 - 3441 - 344
13VALVALAA1 - 3441 - 344
23VALVALDD1 - 3441 - 344
14PROPROBB1 - 3451 - 345
24PROPROCC1 - 3451 - 345
15PROPROBB1 - 3451 - 345
25PROPRODD1 - 3451 - 345
16PROPROCC1 - 3451 - 345
26PROPRODD1 - 3451 - 345

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Alcohol dehydrogenase /


Mass: 36043.914 Da / Num. of mol.: 4 / Mutation: Y54G, L119Y
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) / 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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 1178 / 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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18% (w/v) PAA5100, 0.1 M Tris pH 8, 4 mM NAD+, 10 mM MgCl2, 7.5 mM 4'-Bromo-trifluoroacetophenone, 8 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: 1.83→29.56 Å / Num. obs: 127660 / % possible obs: 98.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 21.84 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.072 / Net I/σ(I): 7.3
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 3 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5876 / CC1/2: 0.524 / Rpim(I) all: 0.509 / % possible all: 91.9

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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: 1.83→29.56 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.064 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19503 6483 5.1 %RANDOM
Rwork0.16802 ---
obs0.16942 121109 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.541 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å2-0 Å20.12 Å2
2--2.1 Å20 Å2
3----0.57 Å2
Refinement stepCycle: 1 / Resolution: 1.83→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9883 0 184 1178 11245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910347
X-RAY DIFFRACTIONr_bond_other_d0.0020.029709
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.98914149
X-RAY DIFFRACTIONr_angle_other_deg0.9443.00222322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.951387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.48722.727363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.471151431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6581574
X-RAY DIFFRACTIONr_chiral_restr0.0780.21649
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111751
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022083
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_it1.6082.7225533
X-RAY DIFFRACTIONr_mcbond_other1.6062.7225532
X-RAY DIFFRACTIONr_mcangle_it2.3554.0776913
X-RAY DIFFRACTIONr_mcangle_other2.3544.0776914
X-RAY DIFFRACTIONr_scbond_it2.1612.9494814
X-RAY DIFFRACTIONr_scbond_other2.1612.9494815
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2824.337233
X-RAY DIFFRACTIONr_long_range_B_refined4.8234.11611547
X-RAY DIFFRACTIONr_long_range_B_other4.77933.9911481
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)
11A207940.04
12B207940.04
21A208060.04
22C208060.04
31A207120.04
32D207120.04
41B208600.04
42C208600.04
51B208700.03
52D208700.03
61C207300.04
62D207300.04
LS refinement shellResolution: 1.832→1.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 484 -
Rwork0.286 8304 -
obs--92.88 %

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