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- PDB-1geg: CRYATAL STRUCTURE ANALYSIS OF MESO-2,3-BUTANEDIOL DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1geg
TitleCRYATAL STRUCTURE ANALYSIS OF MESO-2,3-BUTANEDIOL DEHYDROGENASE
ComponentsACETOIN REDUCTASE
KeywordsOXIDOREDUCTASE / SDR FAMILY
Function / homology
Function and homology information


diacetyl reductase [(S)-acetoin forming] / diacetyl reductase ((S)-acetoin forming) (NAD+) activity / acetoin catabolic process
Similarity search - Function
Acetoin reductase / short chain dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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 / alpha-D-glucopyranose / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Diacetyl reductase [(S)-acetoin forming]
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOtagiri, M. / Kurisu, G. / Ui, S. / Kusunoki, M.
CitationJournal: J.Biochem. / Year: 2001
Title: Crystal structure of meso-2,3-butanediol dehydrogenase in a complex with NAD+ and inhibitor mercaptoethanol at 1.7 A resolution for understanding of chiral substrate recognition mechanisms.
Authors: Otagiri, M. / Kurisu, G. / Ui, S. / Takusagawa, Y. / Ohkuma, M. / Kudo, T. / Kusunoki, M.
History
DepositionNov 10, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2019Group: Data collection / Database references / Category: chem_comp / citation
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETOIN REDUCTASE
B: ACETOIN REDUCTASE
C: ACETOIN REDUCTASE
D: ACETOIN REDUCTASE
E: ACETOIN REDUCTASE
F: ACETOIN REDUCTASE
G: ACETOIN REDUCTASE
H: ACETOIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,41736
Polymers212,9468
Non-polymers7,47128
Water15,115839
1
A: ACETOIN REDUCTASE
B: ACETOIN REDUCTASE
C: ACETOIN REDUCTASE
D: ACETOIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,20918
Polymers106,4734
Non-polymers3,73514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19560 Å2
ΔGint-106 kcal/mol
Surface area31660 Å2
MethodPISA
2
E: ACETOIN REDUCTASE
F: ACETOIN REDUCTASE
G: ACETOIN REDUCTASE
H: ACETOIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,20918
Polymers106,4734
Non-polymers3,73514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19100 Å2
ΔGint-110 kcal/mol
Surface area31450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.160, 109.780, 127.280
Angle α, β, γ (deg.)90.00, 102.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 16 molecules ABCDEFGH

#1: Protein
ACETOIN REDUCTASE


Mass: 26618.299 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Plasmid: PUC119 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q48436, acetoin dehydrogenase
#2: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 859 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 839 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 6000, 100mM HEPES, magnesium chloride, glucose, 2-mercaptoethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG60001reservoir
21 %mercaptoethanol1reservoir
3200 mMmagnesium acetate1reservoir
41 mg/mlNAD+1reservoir
520 %glucose1reservoir
650 mMHEPES1reservoir
710 mg/mlprotein1drop
820 mMTris-HCl1drop
9100 mMmeso-BD1drop
10200 mM1dropNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 203543 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.054
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.192 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 203217 / % possible obs: 100 %
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 100 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→40 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.209 -RANDOM
Rwork0.193 --
all-203217 -
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14904 0 484 839 16227
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.7
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 40 Å / σ(F): 2 / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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