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- PDB-3a28: Crystal structure of L-2,3-butanediol dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 3a28
TitleCrystal structure of L-2,3-butanediol dehydrogenase
ComponentsL-2.3-butanediol dehydrogenase
KeywordsOXIDOREDUCTASE / chiral substrate recognition
Function / homology
Function and homology information


(S,S)-butanediol dehydrogenase / (S,S)-butanediol dehydrogenase activity / acetoin metabolic process / diacetyl reductase [(S)-acetoin forming] / diacetyl reductase ((S)-acetoin forming) (NAD+) activity / butanediol metabolic process / acetoin catabolic process / NADH binding / NAD+ binding / quinone binding ...(S,S)-butanediol dehydrogenase / (S,S)-butanediol dehydrogenase activity / acetoin metabolic process / diacetyl reductase [(S)-acetoin forming] / diacetyl reductase ((S)-acetoin forming) (NAD+) activity / butanediol metabolic process / acetoin catabolic process / NADH binding / NAD+ binding / quinone binding / fatty acid biosynthetic process / protein homotetramerization
Similarity search - Function
Acetoin reductase / 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
BETA-MERCAPTOETHANOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-2,3-butanediol dehydrogenase
Similarity search - Component
Biological speciesBrevibacterium saccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOtagiri, M. / Kurisu, G. / Ui, S. / Kusunoki, M.
CitationJournal: Febs Lett. / Year: 2010
Title: Structural basis for chiral substrate recognition by two 2,3-butanediol dehydrogenases
Authors: Otagiri, M. / Ui, S. / Takusagawa, Y. / Ohtsuki, T. / Kurisu, G. / Kusunoki, M.
History
DepositionMay 2, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: 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_site
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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.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_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

Downloads & links

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Assembly

Deposited unit
C: L-2.3-butanediol dehydrogenase
D: L-2.3-butanediol dehydrogenase
A: L-2.3-butanediol dehydrogenase
B: L-2.3-butanediol dehydrogenase
E: L-2.3-butanediol dehydrogenase
F: L-2.3-butanediol dehydrogenase
G: L-2.3-butanediol dehydrogenase
H: L-2.3-butanediol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,05928
Polymers217,0298
Non-polymers6,03020
Water27,9951554
1
C: L-2.3-butanediol dehydrogenase
D: L-2.3-butanediol dehydrogenase
A: L-2.3-butanediol dehydrogenase
B: L-2.3-butanediol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,52914
Polymers108,5154
Non-polymers3,01510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18960 Å2
ΔGint-135 kcal/mol
Surface area31200 Å2
MethodPISA
2
E: L-2.3-butanediol dehydrogenase
F: L-2.3-butanediol dehydrogenase
G: L-2.3-butanediol dehydrogenase
H: L-2.3-butanediol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,52914
Polymers108,5154
Non-polymers3,01510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18960 Å2
ΔGint-138 kcal/mol
Surface area31170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.8, 69.2, 127.4
Angle α, β, γ (deg.)96.1, 100.2, 109.6
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
L-2.3-butanediol dehydrogenase


Mass: 27128.635 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacterium saccharolyticum (bacteria)
Strain: C-1012 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9ZNN8
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1554 / 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: 45.41 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 18, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 121123 / % possible obs: 94.4 % / Rmerge(I) obs: 0.062

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS0.9refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1geg

1geg


Resolution: 2→30 Å / Stereochemistry target values: Engh & Huber /
RfactorNum. reflection
Rfree0.24 -
Rwork0.193 -
obs-121123
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15208 0 388 1554 17150

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