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- PDB-6ie0: X-ray crystal structure of 2R,3R-butanediol dehydrogenase from Ba... -

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Basic information

Entry
Database: PDB / ID: 6ie0
TitleX-ray crystal structure of 2R,3R-butanediol dehydrogenase from Bacillus subtilis
Components(R,R)-butanediol dehydrogenase(R,R)-butanediol dehydrogenase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


(R,R)-butanediol dehydrogenase / (R,R)-butanediol dehydrogenase activity / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / 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 ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(R,R)-butanediol dehydrogenase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.976 Å
AuthorsWang, X.F. / Feng, Y.B. / Ji, F.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)21506025 China
CitationJournal: To Be Published
Title: X-ray crystal structure of 2R,3R-butanediol dehydrogenase from Bacillus subtilis
Authors: Wang, X.F. / Feng, Y.B. / Ji, F.L.
History
DepositionSep 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (R,R)-butanediol dehydrogenase
B: (R,R)-butanediol dehydrogenase
C: (R,R)-butanediol dehydrogenase
D: (R,R)-butanediol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,1498
Polymers149,8874
Non-polymers2624
Water0
1
A: (R,R)-butanediol dehydrogenase
C: (R,R)-butanediol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0744
Polymers74,9442
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-89 kcal/mol
Surface area27590 Å2
MethodPISA
2
B: (R,R)-butanediol dehydrogenase
D: (R,R)-butanediol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0744
Polymers74,9442
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-89 kcal/mol
Surface area27560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.839, 200.839, 83.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
(R,R)-butanediol dehydrogenase / (R,R)-butanediol dehydrogenase / 2R / 3R-butanediol dehydrogenase


Mass: 37471.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O34788, (R,R)-butanediol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 277 K / Method: evaporation / Details: PEG3350, magnesium formate dihydrate, BOG

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.976→48.711 Å / Num. obs: 34586 / % possible obs: 97.46 % / Redundancy: 25.9 % / Net I/σ(I): 33.93
Reflection shellResolution: 2.976→3 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.976→48.711 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.47
RfactorNum. reflection% reflection
Rfree0.2277 1793 5.18 %
Rwork0.172 --
obs0.1749 34586 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.976→48.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10548 0 4 0 10552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510748
X-RAY DIFFRACTIONf_angle_d0.90914560
X-RAY DIFFRACTIONf_dihedral_angle_d6.8146452
X-RAY DIFFRACTIONf_chiral_restr0.0561664
X-RAY DIFFRACTIONf_plane_restr0.0051888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9763-3.05680.3311340.24372380X-RAY DIFFRACTION94
3.0568-3.14670.32791290.23672425X-RAY DIFFRACTION96
3.1467-3.24830.3251480.21752464X-RAY DIFFRACTION98
3.2483-3.36440.2681540.21382491X-RAY DIFFRACTION98
3.3644-3.4990.27221370.19772534X-RAY DIFFRACTION99
3.499-3.65820.27971370.19862528X-RAY DIFFRACTION99
3.6582-3.8510.22411450.17582537X-RAY DIFFRACTION99
3.851-4.09220.22641150.17222563X-RAY DIFFRACTION99
4.0922-4.40790.20281260.13922586X-RAY DIFFRACTION99
4.4079-4.85120.17311300.12982579X-RAY DIFFRACTION99
4.8512-5.55230.20611350.1442559X-RAY DIFFRACTION98
5.5523-6.9920.22561490.17632552X-RAY DIFFRACTION97
6.992-48.71710.16311540.15532595X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: -48.9285 Å / Origin y: -1.7215 Å / Origin z: 13.9582 Å
111213212223313233
T0.2344 Å2-0.0003 Å2-0.0425 Å2-0.2447 Å20.0087 Å2--0.2649 Å2
L0.2948 °20.0516 °2-0.0512 °2-0.3438 °20.0633 °2--0.6505 °2
S0.0105 Å °-0.0149 Å °-0.0089 Å °-0.0321 Å °-0.0019 Å °0.0954 Å °0.1006 Å °-0.2221 Å °-0.0055 Å °
Refinement TLS groupSelection details: all

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