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- PDB-5z2x: Structure of Alcohol dehydrogenase from Kluyveromyces polyspora(KpADH) -

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Basic information

Entry
Database: PDB / ID: 5z2x
TitleStructure of Alcohol dehydrogenase from Kluyveromyces polyspora(KpADH)
ComponentsAlcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Alcohol dehydrogenase(KpADH) / NADPH
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
: / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / NAD-dependent epimerase/dehydratase domain-containing protein
Similarity search - Component
Biological speciesVanderwaltozyma polyspora DSM 70294 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsWang, Y. / Zhou, J.Y. / Hou, X.D. / Xu, G.C. / Wu, L. / Rao, Y.J. / ZHou, J.H. / Ni, Y.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China grant number21506073 China
National Natural Science Foundation of China grant number21776112 China
Natural Science Foundation of Jiangsu ProvinceBK20150003 China
Natural Science Foundation of Jiangsu ProvinceBK20171135 China
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Structural Insight into Enantioselective Inversion of an Alcohol Dehydrogenase Reveals a "Polar Gate" in Stereorecognition of Diaryl Ketones.
Authors: Zhou, J.Y. / Wang, Y. / Xu, G.C. / Wu, L. / Han, R.Z. / Schwaneberg, U. / Rao, Y.J. / Zhao, Y.L. / Zhou, J.H. / Ni, Y.
History
DepositionJan 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Alcohol dehydrogenase
B: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,16814
Polymers77,8982
Non-polymers2,27012
Water9,296516
1
A: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2019
Polymers38,9491
Non-polymers1,2528
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint6 kcal/mol
Surface area14520 Å2
MethodPISA
2
B: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9675
Polymers38,9491
Non-polymers1,0184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint7 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.652, 102.652, 134.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 1 - 342 / Label seq-ID: 1 - 342

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase


Mass: 38949.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vanderwaltozyma polyspora DSM 70294 (fungus)
Strain: ATCC 22028 / DSM 70294 / Gene: Kpol_529p27 / Plasmid: pET28a / Cell (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A7TM80, alcohol dehydrogenase (NADP+)

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Non-polymers , 5 types, 528 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: ammonium acetate, HEPES,31%PEG3350 / PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.9796→50 Å / Num. obs: 55577 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 24.09 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 19.92
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 4.778 / Num. unique obs: 571154 / Rsym value: 0.487 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.12-2829refinement
HKL-3000data reduction
PHENIX1.12-2829phasing
PHENIX1.12-2829model building
PDB_EXTRACT3.24data extraction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PVC

4pvc


Resolution: 1.98→33.706 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.39
RfactorNum. reflection% reflection
Rfree0.1904 2948 5.3 %
Rwork0.1589 --
obs0.1606 55576 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.05 Å2 / Biso mean: 26.5025 Å2 / Biso min: 14.73 Å2
Refinement stepCycle: final / Resolution: 1.98→33.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 0 147 516 6153
Biso mean--27.41 31.18 -
Num. residues----684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085757
X-RAY DIFFRACTIONf_angle_d0.9427790
X-RAY DIFFRACTIONf_chiral_restr0.057868
X-RAY DIFFRACTIONf_plane_restr0.007990
X-RAY DIFFRACTIONf_dihedral_angle_d6.9953423
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3312X-RAY DIFFRACTION5.624TORSIONAL
12B3312X-RAY DIFFRACTION5.624TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9796-2.0120.24911510.188224702621100
2.012-2.04670.26131170.188325212638100
2.0467-2.08390.2551400.188424982638100
2.0839-2.1240.22961550.174424552610100
2.124-2.16740.23141410.173225302671100
2.1674-2.21450.20921210.167725012622100
2.2145-2.2660.20611610.162324962657100
2.266-2.32260.23061540.157524822636100
2.3226-2.38540.20651490.164725262675100
2.3854-2.45560.18281050.160825232628100
2.4556-2.53480.20311370.160424872624100
2.5348-2.62540.22521560.157425102666100
2.6254-2.73050.20211170.165425342651100
2.7305-2.85470.22451370.169325252662100
2.8547-3.00510.19571510.173924912642100
3.0051-3.19320.18951370.17125172654100
3.1932-3.43960.1731490.164825012650100
3.4396-3.78530.20141360.150525232659100
3.7853-4.33210.15451350.137225212656100
4.3321-5.45420.12661690.13325002669100
5.4542-33.71050.18741300.15462517264798
Refinement TLS params.Method: refined / Origin x: -25.2937 Å / Origin y: 133.1351 Å / Origin z: -1.9789 Å
111213212223313233
T0.1976 Å20.0146 Å2-0.0007 Å2-0.1854 Å20.0005 Å2--0.1651 Å2
L0.7337 °20.251 °2-0.0406 °2-0.4145 °2-0.0446 °2--0.0656 °2
S0.0151 Å °-0.0785 Å °-0.0013 Å °0.0267 Å °-0.0307 Å °-0.0152 Å °-0.0182 Å °0.0029 Å °0.016 Å °
Refinement TLS groupSelection details: all

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