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- PDB-5yho: Crystal structure of acetolactate decarboxylase from Enterobacter... -

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Basic information

Entry
Database: PDB / ID: 5yho
TitleCrystal structure of acetolactate decarboxylase from Enterobacter cloacae
ComponentsAlpha-acetolactate decarboxylase
KeywordsMETAL BINDING PROTEIN / acetolactate decarboxylase Enterobacter cloacae
Function / homology
Function and homology information


acetolactate decarboxylase / acetoin biosynthetic process / acetolactate decarboxylase activity
Similarity search - Function
Alpha-acetolactate decarboxylase / Alpha-acetolactate decarboxylase / Hypothetical protein, similar to alpha- acetolactate decarboxylase; domain 2 / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-acetolactate decarboxylase
Similarity search - Component
Biological speciesKlebsiella aerogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsJi, F.L. / Li, M.Y. / Feng, Y.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)21506025 China
CitationJournal: To Be Published
Title: Crystal structure of acetolactate decarboxylase from Enterobacter cloacae
Authors: Ji, F.L. / Li, M.Y. / Feng, Y.B.
History
DepositionSep 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _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.ptnr1_label_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-acetolactate decarboxylase
B: Alpha-acetolactate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6276
Polymers53,4262
Non-polymers2024
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-123 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.832, 59.981, 80.818
Angle α, β, γ (deg.)90.00, 108.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-acetolactate decarboxylase


Mass: 26712.807 Da / Num. of mol.: 2 / Fragment: UNP residues 23-260 / Mutation: K24Q, D47E, A114T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: budA, aldC / Production host: Escherichia coli (E. coli) / References: UniProt: P05361, acetolactate decarboxylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 1.98 Å3/Da / Density % sol: 38.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium acetate trihydrate pH4.5 3.0M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9798 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.401→47.27 Å / Num. obs: 16057 / % possible obs: 97.69 % / Redundancy: 4 % / Net I/σ(I): 23.46

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.401→47.27 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.44
RfactorNum. reflection% reflection
Rfree0.2719 740 4.61 %
Rwork0.2105 --
obs0.2134 16044 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.401→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 2 111 3857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043834
X-RAY DIFFRACTIONf_angle_d0.9675208
X-RAY DIFFRACTIONf_dihedral_angle_d16.0211398
X-RAY DIFFRACTIONf_chiral_restr0.039563
X-RAY DIFFRACTIONf_plane_restr0.004701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4012-2.58660.25811270.22162905X-RAY DIFFRACTION94
2.5866-2.84680.31571510.24053095X-RAY DIFFRACTION99
2.8468-3.25870.32861490.22963100X-RAY DIFFRACTION99
3.2587-4.10530.24731450.20013092X-RAY DIFFRACTION99
4.1053-47.27880.25691680.1963112X-RAY DIFFRACTION97

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