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- PDB-5xne: X-ray Crystal Structure of alpha-acetolactate decarboxylase from ... -

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Basic information

Entry
Database: PDB / ID: 5xne
TitleX-ray Crystal Structure of alpha-acetolactate decarboxylase from Bacillus subtilis strain 168
ComponentsAlpha-acetolactate decarboxylase
KeywordsLYASE / Acetolactate decarboxylase
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 speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsJi, F. / Li, M. / Feng, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21506025 China
Dalian University of TechnologyDUT16RC(4)12 China
CitationJournal: Appl. Microbiol. Biotechnol. / Year: 2018
Title: Structural and enzymatic characterization of acetolactate decarboxylase from Bacillus subtilis
Authors: Ji, F. / Li, M. / Feng, Y. / Wu, S. / Wang, T. / Pu, Z. / Wang, J. / Yang, Y. / Xue, S. / Bao, Y.
History
DepositionMay 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Alpha-acetolactate decarboxylase
A: Alpha-acetolactate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1344
Polymers53,0032
Non-polymers1312
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-86 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.303, 71.303, 84.134
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Alpha-acetolactate decarboxylase


Mass: 26501.639 Da / Num. of mol.: 2 / Fragment: UNP residues 19-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: alsD, BSU36000
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q04777, acetolactate decarboxylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 277 K / Method: evaporation / Details: 0.1M tris, pH8.5, 0.2M NaCl, 25% PEG 3350, 1% BOG

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1.0001 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 1.5→49.781 Å / Num. obs: 123611 / % possible obs: 99.8 % / Redundancy: 6.6 % / Net I/σ(I): 33.93

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BT7

4bt7


Resolution: 1.501→49.781 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.16
RfactorNum. reflection% reflection
Rfree0.2265 3296 2.67 %
Rwork0.1964 --
obs0.1972 123611 80.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.501→49.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3721 0 2 491 4214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083806
X-RAY DIFFRACTIONf_angle_d1.1175151
X-RAY DIFFRACTIONf_dihedral_angle_d13.3041389
X-RAY DIFFRACTIONf_chiral_restr0.045558
X-RAY DIFFRACTIONf_plane_restr0.005684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.501-1.52240.2356880.24593075X-RAY DIFFRACTION49
1.5224-1.54510.2728810.2373068X-RAY DIFFRACTION50
1.5451-1.56930.3893850.24283079X-RAY DIFFRACTION50
1.5693-1.5950.2336870.2253080X-RAY DIFFRACTION50
1.595-1.62250.3293870.22963180X-RAY DIFFRACTION50
1.6225-1.6520.2352800.22933175X-RAY DIFFRACTION51
1.652-1.68380.2017950.23233392X-RAY DIFFRACTION56
1.6838-1.71820.23731150.20293970X-RAY DIFFRACTION64
1.7182-1.75550.20851310.20294522X-RAY DIFFRACTION73
1.7555-1.79640.26761550.19425213X-RAY DIFFRACTION84
1.7964-1.84130.23471360.20215572X-RAY DIFFRACTION89
1.8413-1.89110.24831540.22045696X-RAY DIFFRACTION93
1.8911-1.94670.20991710.21266096X-RAY DIFFRACTION98
1.9467-2.00960.24561710.20386099X-RAY DIFFRACTION98
2.0096-2.08140.28851610.19576095X-RAY DIFFRACTION99
2.0814-2.16470.24311700.19236165X-RAY DIFFRACTION98
2.1647-2.26330.18761680.18486018X-RAY DIFFRACTION98
2.2633-2.38260.25171660.19776034X-RAY DIFFRACTION97
2.3826-2.53180.24861520.20536163X-RAY DIFFRACTION99
2.5318-2.72730.24331670.1966238X-RAY DIFFRACTION100
2.7273-3.00170.21341820.20336149X-RAY DIFFRACTION100
3.0017-3.4360.20131540.19216053X-RAY DIFFRACTION97
3.436-4.32860.23351770.17316017X-RAY DIFFRACTION98
4.3286-49.80840.16741630.18276166X-RAY DIFFRACTION99

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