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- PDB-5o9f: Crystal structure of R. ruber ADH-A, mutant Y294F, W295A, Y54F, F... -

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Basic information

Entry
Database: PDB / ID: 5o9f
TitleCrystal structure of R. ruber ADH-A, mutant Y294F, W295A, Y54F, F43S, 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
(2~{S})-2-methylpentanedioic acid / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase
Similarity search - Component
Biological speciesRhodococcus sp. M8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsDobritzsch, D. / Maurer, D. / Hamnevik, E. / Enugala, T.R. / 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 19, 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 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.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_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)147,35119
Polymers143,7354
Non-polymers3,61515
Water29,0401612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15200 Å2
ΔGint-254 kcal/mol
Surface area45170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.842, 105.293, 109.287
Angle α, β, γ (deg.)90.00, 91.36, 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
12VALVALAA1 - 3441 - 344
22VALVALCC1 - 3441 - 344
13THRTHRAA1 - 3461 - 346
23THRTHRDD1 - 3461 - 346
14VALVALBB1 - 3441 - 344
24VALVALCC1 - 3441 - 344
15THRTHRBB1 - 3461 - 346
25THRTHRDD1 - 3461 - 346
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: 35933.820 Da / Num. of mol.: 4 / Mutation: Y294F, W295A, Y54F, F43S, H39Y
Source method: isolated from a genetically manipulated source
Details: contains four mutations compared to wildtype enzyme C-terminally his-tagged
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 / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-9ON / (2~{S})-2-methylpentanedioic acid


Mass: 146.141 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H10O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1612 / 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: 2.31 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PAA5100, 0.1 M Tris pH 8, 4 mM NAD+, 1 mM MgCl2, 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: 1.64→29.53 Å / Num. obs: 177639 / % possible obs: 97.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 16 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.05 / Net I/σ(I): 7.1
Reflection shellResolution: 1.64→1.66 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6166 / CC1/2: 0.66 / Rpim(I) all: 0.393 / % possible all: 68.7

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Processing

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

3jv7


Resolution: 1.64→29.5 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.309 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.082 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18556 8693 4.9 %RANDOM
Rwork0.16793 ---
obs0.16881 168316 97.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.418 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0 Å20.35 Å2
2--0.68 Å2-0 Å2
3----0.87 Å2
Refinement stepCycle: 1 / Resolution: 1.64→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9859 0 214 1612 11685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910319
X-RAY DIFFRACTIONr_bond_other_d0.0020.029729
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.99414122
X-RAY DIFFRACTIONr_angle_other_deg0.94322409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74551395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64322.789355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31151439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4461574
X-RAY DIFFRACTIONr_chiral_restr0.0780.21666
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111739
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_it0.5941.4675542
X-RAY DIFFRACTIONr_mcbond_other0.5941.4675541
X-RAY DIFFRACTIONr_mcangle_it0.9842.1996925
X-RAY DIFFRACTIONr_mcangle_other0.9842.1996926
X-RAY DIFFRACTIONr_scbond_it0.8931.5994777
X-RAY DIFFRACTIONr_scbond_other0.8931.64778
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4212.3567188
X-RAY DIFFRACTIONr_long_range_B_refined5.35520.69711780
X-RAY DIFFRACTIONr_long_range_B_other5.35620.69511780
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)
11A206540.05
12B206540.05
21A204040.05
22C204040.05
31A205840.05
32D205840.05
41B203240.04
42C203240.04
51B205700.04
52D205700.04
61C203400.05
62D203400.05
LS refinement shellResolution: 1.64→1.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 493 -
Rwork0.3 9939 -
obs--77.68 %
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)
10.70770.26520.13060.94080.21061.3240.0005-0.03190.10150.0571-0.0136-0.045-0.15010.0590.01310.0312-0.0146-0.00990.0104-0.00110.024290.243812.5268249.5581
20.6766-0.1543-0.05680.8330.20271.1741-0.01880.0336-0.1376-0.0473-0.0121-0.04150.14740.03130.0310.02670.00490.01430.0034-0.00470.036387.6023-28.6619241.8932
34.51241.8212-0.83724.8907-1.70431.57250.0158-0.68320.15910.76590.11840.3789-0.1008-0.1434-0.13420.44560.00790.05530.58960.02980.184256.8908-3.0517285.4926
41.3818-0.48940.84924.2533-1.43752.8204-0.1324-0.63980.05580.37940.152-0.2704-0.2943-0.1978-0.01960.29040.09360.08860.463-0.03930.224260.4563-1.7728276.292
55.1457-1.0201-0.37752.28270.26392.2216-0.1786-0.7122-0.18290.43990.12060.1905-0.2018-0.14290.0580.15840.03580.02820.14290.0090.025269.3646-1.4594270.3602
61.2090.00770.97142.2901-0.03212.7982-0.1455-0.25640.15130.36680.17990.153-0.2672-0.2402-0.03440.08980.05370.01260.093-0.00470.047660.9355-3.2834259.9474
71.69970.0933-0.14231.7309-0.05690.9268-0.0043-0.0564-0.1625-0.07530.03430.23320.1022-0.1699-0.030.0144-0.0225-0.01440.05380.01990.051358.7701-18.9842254.5083
81.35730.2819-0.45370.9671-0.93423.8590.04-0.3414-0.00970.21210.1550.2385-0.0051-0.3018-0.1950.23820.01460.1050.39490.00650.294147.2935-8.8412270.8092
91.0664-0.43270.09441.10130.2750.97820.05180.3423-0.086-0.3122-0.05840.09710.0441-0.04860.00660.1169-0.027-0.02860.1323-0.01450.030763.682-8.6577219.1958
104.70521.04690.03334.11390.09381.95040.0155-0.0320.30430.0882-0.08470.1961-0.2093-0.16790.06920.03340.03520.00530.07120.03140.073953.612712.4828235.9552
111.1468-0.00560.34161.27040.22491.0203-0.0090.20240.0945-0.20950.00170.1958-0.0657-0.08690.00730.03560.0034-0.03130.06550.02720.041761.81023.2473227.0758
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 346
2X-RAY DIFFRACTION2B1 - 346
3X-RAY DIFFRACTION3C1 - 26
4X-RAY DIFFRACTION4C27 - 80
5X-RAY DIFFRACTION5C81 - 128
6X-RAY DIFFRACTION6C129 - 175
7X-RAY DIFFRACTION7C176 - 311
8X-RAY DIFFRACTION8C312 - 346
9X-RAY DIFFRACTION9D1 - 197
10X-RAY DIFFRACTION10D198 - 238
11X-RAY DIFFRACTION11D239 - 346

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