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- PDB-6qhe: Alcohol Dehydrogenase from Arthrobacter sp. TS-15 in complex with NAD+ -

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Basic information

Entry
Database: PDB / ID: 6qhe
TitleAlcohol Dehydrogenase from Arthrobacter sp. TS-15 in complex with NAD+
ComponentsAlcohol Dehydrogenase
KeywordsOXIDOREDUCTASE / Oxidroreductase / Dehydrogenase / Ketoreductase / SDR / NAD
Function / homologyEnoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Pseudoephedrine dehydrogenase
Function and homology information
Biological speciesArthrobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsLockie, C. / Beloti, L. / Shanati, T. / Ansorge-Schumacher, M. / Grogan, G.
CitationJournal: Acs Catalysis / Year: 2019
Title: Two Enantiocomplementary Ephedrine Dehydrogenases from Arthrobacter sp. TS-15 with Broad Substrate Specificity
Authors: Shanati, T. / Lockie, C. / Beloti, L. / Grogan, G. / Ansorge-Schumacher, M.
History
DepositionJan 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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_conn.ptnr2_symmetry / _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
E: Alcohol Dehydrogenase
F: Alcohol Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,58215
Polymers172,1736
Non-polymers3,4099
Water13,962775
1
A: Alcohol Dehydrogenase
C: Alcohol Dehydrogenase
D: Alcohol Dehydrogenase
F: Alcohol Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,48210
Polymers114,7824
Non-polymers2,7006
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20360 Å2
ΔGint-175 kcal/mol
Surface area31550 Å2
MethodPISA
2
B: Alcohol Dehydrogenase
E: Alcohol Dehydrogenase
hetero molecules

B: Alcohol Dehydrogenase
E: Alcohol Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,20110
Polymers114,7824
Non-polymers1,4196
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area18080 Å2
ΔGint-180 kcal/mol
Surface area31460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.731, 119.041, 348.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-301-

NA

21B-499-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13B
23D
14B
24E
15B
25F
16A
26C
17A
27D
18A
28E
19A
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLUBB1 - 2572 - 258
21METMETGLUGLUAA1 - 2572 - 258
12METMETGLUGLUBB1 - 2572 - 258
22METMETGLUGLUCC1 - 2572 - 258
13METMETGLUGLUBB1 - 2572 - 258
23METMETGLUGLUDD1 - 2572 - 258
14METMETTYRTYRBB1 - 2582 - 259
24METMETTYRTYREE1 - 2582 - 259
15METMETGLUGLUBB1 - 2572 - 258
25METMETGLUGLUFF1 - 2572 - 258
16HISHISGLUGLUAA0 - 2571 - 258
26HISHISGLUGLUCC0 - 2571 - 258
17HISHISTYRTYRAA0 - 2581 - 259
27HISHISTYRTYRDD0 - 2581 - 259
18METMETGLUGLUAA1 - 2572 - 258
28METMETGLUGLUEE1 - 2572 - 258
19HISHISGLUGLUAA0 - 2571 - 258
29HISHISGLUGLUFF0 - 2571 - 258
110HISHISGLUGLUCC0 - 2571 - 258
210HISHISGLUGLUDD0 - 2571 - 258
111METMETGLUGLUCC1 - 2572 - 258
211METMETGLUGLUEE1 - 2572 - 258
112HISHISTYRTYRCC0 - 2581 - 259
212HISHISTYRTYRFF0 - 2581 - 259
113METMETGLUGLUDD1 - 2572 - 258
213METMETGLUGLUEE1 - 2572 - 258
114HISHISGLUGLUDD0 - 2571 - 258
214HISHISGLUGLUFF0 - 2571 - 258
115METMETGLUGLUEE1 - 2572 - 258
215METMETGLUGLUFF1 - 2572 - 258

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Alcohol Dehydrogenase /


Mass: 28695.512 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter (bacteria) / Variant: TS-15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A545BBS8*PLUS, alcohol dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 1.97 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM bis-Tris pH 5.5; 25% (w/v) PEG 3350; 200 mM MgCL2; 5 mM NAD+

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.83→52.92 Å / Num. obs: 147773 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 25 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.04 / Net I/σ(I): 16.8
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 7240 / CC1/2: 0.84 / Rpim(I) all: 0.42 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VL8

1vl8


Resolution: 1.83→48.28 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.445 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18166 7349 5 %RANDOM
Rwork0.15947 ---
obs0.16059 140332 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.507 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-0 Å2
2--1.69 Å20 Å2
3----1.98 Å2
Refinement stepCycle: 1 / Resolution: 1.83→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11302 0 224 776 12302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01311788
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710901
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.62516075
X-RAY DIFFRACTIONr_angle_other_deg1.511.57525165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99251578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.8522.77527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.815151793
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3041566
X-RAY DIFFRACTIONr_chiral_restr0.0830.21644
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022356
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_it2.5312.9136243
X-RAY DIFFRACTIONr_mcbond_other2.5262.9136242
X-RAY DIFFRACTIONr_mcangle_it3.1674.357799
X-RAY DIFFRACTIONr_mcangle_other3.1674.3517800
X-RAY DIFFRACTIONr_scbond_it3.7273.2485545
X-RAY DIFFRACTIONr_scbond_other3.7273.2485546
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.214.7418262
X-RAY DIFFRACTIONr_long_range_B_refined6.01136.14913092
X-RAY DIFFRACTIONr_long_range_B_other5.97535.93812949
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)
11B77000.06
12A77000.06
21B77200.07
22C77200.07
31B75990.09
32D75990.09
41B76810.08
42E76810.08
51B77570.07
52F77570.07
61A78000.07
62C78000.07
71A77170.09
72D77170.09
81A77430.08
82E77430.08
91A77870.07
92F77870.07
101C75760.09
102D75760.09
111C76580.08
112E76580.08
121C77650.07
122F77650.07
131D75600.1
132E75600.1
141D76390.09
142F76390.09
151E76180.09
152F76180.09
LS refinement shellResolution: 1.83→1.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 532 -
Rwork0.237 10308 -
obs--99.97 %

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