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- PDB-3wye: Crystal Structure of chimeric engineered (2S,3S)-butanediol dehyd... -

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Basic information

Entry
Database: PDB / ID: 3wye
TitleCrystal Structure of chimeric engineered (2S,3S)-butanediol dehydrogenase complexed with NAD+
ComponentsDiacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming]
KeywordsOXIDOREDUCTASE / butanediol dehydrogenase / domain chimera / NAD+ complex / short-chain dehydrogenase/reductase family / Rossmann Fold / NAD+ Binding / Oxidation/reduction
Function / homology
Function and homology information


(S,S)-butanediol dehydrogenase / acetoin metabolic process / (S,S)-butanediol dehydrogenase activity / diacetyl reductase [(S)-acetoin forming] / diacetyl reductase ((S)-acetoin forming) (NAD+) activity / butanediol metabolic process / acetoin catabolic process / NADH binding / NAD+ binding / protein homotetramerization
Similarity search - Function
Acetoin reductase / short chain dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...Acetoin reductase / short chain dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(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
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Diacetyl reductase [(S)-acetoin forming] / L-2,3-butanediol dehydrogenase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
Corynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsShimegi, T. / Oyama, T. / Kusunoki, M. / Ui, S.
CitationJournal: To be Published
Title: Crystal Structure of chimeric engineered (2S,3S)-butanediol dehydrogenase complexed with NAD+
Authors: Shimegi, T. / Oyama, T. / Kusunoki, M. / Ui, S.
History
DepositionAug 26, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Structure summary / Category: entity / Item: _entity.pdbx_mutation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming]
B: Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7684
Polymers53,4412
Non-polymers1,3272
Water2,522140
1
A: Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming]
B: Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming]
hetero molecules

A: Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming]
B: Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5358
Polymers106,8824
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area17800 Å2
ΔGint-101 kcal/mol
Surface area30740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.244, 134.617, 87.794
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by two fold symmetry operation: x, -y, -z.

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Components

#1: Protein Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming] / Acetoin(diacetyl) reductase / AR / Meso-2 / 3-butanediol dehydrogenase / L-BDH / (S / S)-butanediol ...Acetoin(diacetyl) reductase / AR / Meso-2 / 3-butanediol dehydrogenase / L-BDH / (S / S)-butanediol dehydrogenase / Diacetyl reductase [(S)-acetoin forming] / Acetoin(diacetyl) reductase / AR / Meso-2 / 3-butanediol dehydrogenase / L-BDH / (S / S)-butanediol dehydrogenase / Diacetyl reductase [(S)-acetoin forming] / Acetoin(diacetyl) reductase / AR / Meso-2 / 3-butanediol dehydrogenase / L-BDH / (S / S)-butanediol dehydrogenase / Diacetyl reductase [(S)-acetoin forming] / Acetoin(diacetyl) reductase / AR / Meso-2 / 3-butanediol dehydrogenase


Mass: 26720.445 Da / Num. of mol.: 2
Mutation: R52H, M54V,R52H, M54V,R52H, M54V,R52H, M54V,R52H, M54V,R52H, M54V,R52H, M54V
Source method: isolated from a genetically manipulated source
Details: Residues 84-118, 135-161 and 182-236 derived from Corynebacterium glutamicum (2S,3S)-butanediol dehydrogenase and the remaining resides from Klebsiella pneumoniae (2R,3S)-butanediol dehydrogenase
Source: (gene. exp.) Klebsiella pneumoniae (bacteria), (gene. exp.) Corynebacterium glutamicum (bacteria)
Gene: budC / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q48436, UniProt: Q9ZNN8, diacetyl reductase [(S)-acetoin forming], (S,S)-butanediol dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.25 Å3/Da / Density % sol: 45.23 % / Mosaicity: 0.532 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 17% PEG6000, 100mM MES, 15% glycerol, 1% 2-mercaptoethanol, pH 6.4, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 26, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.578→50 Å / Num. obs: 65845 / % possible obs: 99.4 % / Redundancy: 8.9 % / Biso Wilson estimate: 18.88 Å2 / Rmerge(I) obs: 0.051 / Χ2: 1.027 / Net I/σ(I): 19.2
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.58-1.616.40.25332211.09198.5
1.61-1.6470.23632401.10498.6
1.64-1.677.40.21632311.10998.8
1.67-1.77.40.18932291.14598.9
1.7-1.747.40.16632591.09999.1
1.74-1.787.40.14832361.09499.2
1.78-1.827.40.12232751.10599.4
1.82-1.877.40.10633001.09899.4
1.87-1.937.40.09232331.09899.4
1.93-1.997.50.07932601.0299.3
1.99-2.067.40.06832931.02899.6
2.06-2.147.40.06133040.93799.5
2.14-2.247.50.05432750.97599.8
2.24-2.367.40.0532911.06299.6
2.36-2.517.40.04533020.98399.7
2.51-2.712.40.06333280.97299.8
2.7-2.9714.70.05833171.09199.9
2.97-3.414.40.04833610.991100
3.4-4.2913.60.04233810.92100
4.29-5012.20.04435090.88499.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→39.279 Å / SU ML: 0.13 / Isotropic thermal model: Isotropic / σ(F): 1.35 / Phase error: 20.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1988 3338 5.07 %RANDOM
Rwork0.182 ---
obs0.1829 65801 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.04 Å2 / Biso mean: 25.5213 Å2 / Biso min: 13.09 Å2
Refinement stepCycle: LAST / Resolution: 1.58→39.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3619 0 88 140 3847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043797
X-RAY DIFFRACTIONf_angle_d0.9245168
X-RAY DIFFRACTIONf_chiral_restr0.036606
X-RAY DIFFRACTIONf_plane_restr0.004664
X-RAY DIFFRACTIONf_dihedral_angle_d16.1331361
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5782-1.60080.25121220.20332468259094
1.6008-1.62470.22431450.20012530267598
1.6247-1.65010.22141530.19112540269399
1.6501-1.67710.20221470.192572271999
1.6771-1.7060.21681270.19172584271199
1.706-1.73710.21341340.18582564269899
1.7371-1.77050.22231350.19282571270699
1.7705-1.80660.20811440.18252591273599
1.8066-1.84590.21981380.18372576271499
1.8459-1.88880.21491470.1852565271299
1.8888-1.93610.19831590.18452601276099
1.9361-1.98840.21461290.186625802709100
1.9884-2.04690.20431370.191726022739100
2.0469-2.1130.20321200.200326232743100
2.113-2.18850.21421420.190526032745100
2.1885-2.27610.21031400.188325902730100
2.2761-2.37970.20071430.187226272770100
2.3797-2.50510.1941390.190826092748100
2.5051-2.66210.24451290.190426312760100
2.6621-2.86750.19141470.204526302777100
2.8675-3.1560.18751250.186926932818100
3.156-3.61240.22661330.182526512784100
3.6124-4.55020.16521540.156326792833100
4.5502-39.29150.17231490.16182783293299

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