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- PDB-6pwq: Crystal structure of Levansucrase from Bacillus subtilis mutant S... -

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Basic information

Entry
Database: PDB / ID: 6pwq
TitleCrystal structure of Levansucrase from Bacillus subtilis mutant S164A at 2.6 A
ComponentsGlycoside hydrolase family 68 protein
KeywordsTRANSFERASE / Levansucrase / Glycoside hydrolase / Levan / Fructose polymers
Function / homology
Function and homology information


levansucrase / levansucrase activity / carbohydrate utilization / extracellular region / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 68 / Levansucrase/Invertase / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily
Similarity search - Domain/homology
Levansucrase / Levansucrase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDiaz-Vilchis, A. / Rodriguez-Alegria, M.E. / Ortiz-Soto, M.E. / Rudino-Pinera, E. / Lopez-Munguia, A.
Funding support Mexico, Germany, 3items
OrganizationGrant numberCountry
Other governmentCONACyT-BMBF- 2015-267620. Mexico
Other governmentBundesministerium fur Bildung und Forschung (01DN16034). Germany
Other governmentInstituto de Biotecnologia, UNAM. Institutional budget. Mexico
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Implications of the mutation S164A on Bacillus subtilis levansucrase product specificity and insights into protein interactions acting upon levan synthesis.
Authors: Ortiz-Soto, M.E. / Porras-Dominguez, J.R. / Rodriguez-Alegria, M.E. / Morales-Moreno, L.A. / Diaz-Vilchis, A. / Rudino-Pinera, E. / Beltran-Hernandez, N.E. / Rivera, H.M. / Seibel, J. / Lopez Munguia, A.
History
DepositionJul 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
A: Glycoside hydrolase family 68 protein
B: Glycoside hydrolase family 68 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,74431
Polymers104,8942
Non-polymers2,85029
Water3,369187
1
A: Glycoside hydrolase family 68 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,82615
Polymers52,4471
Non-polymers1,37914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 68 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,91816
Polymers52,4471
Non-polymers1,47115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.535, 109.535, 204.468
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycoside hydrolase family 68 protein / Levansucrase


Mass: 52446.844 Da / Num. of mol.: 2 / Mutation: S164A
Source method: isolated from a genetically manipulated source
Details: Calcium Sulfate Tetraethylene Glycol Glycerol / Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: sacB, B4417_3269, ETA10_18085, ETL41_09350 / Plasmid: pET22b+ / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0PFL2, UniProt: P05655*PLUS

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Non-polymers , 5 types, 216 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.1 Å3/Da / Density % sol: 60.36 % / Description: irregular octahedron
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 3.2 M ammonium sulfate and 100 mM citric acid/sodium hydroxide, pH 5.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.02 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 38955 / % possible obs: 99.9 % / Observed criterion σ(I): 3.1 / Redundancy: 6.8 % / Biso Wilson estimate: 45.9 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.5
Reflection shellResolution: 2.6→2.71 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3808 / CC1/2: 0.81 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OYG

1oyg


Resolution: 2.6→19.9782 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.43
RfactorNum. reflection% reflection
Rfree0.239 2000 5.13 %
Rwork0.1835 --
obs0.1863 38952 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.68 Å2 / Biso mean: 48.7225 Å2 / Biso min: 29.13 Å2
Refinement stepCycle: final / Resolution: 2.6→19.9782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6965 0 158 187 7310
Biso mean--69.06 45.51 -
Num. residues----878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067246
X-RAY DIFFRACTIONf_angle_d0.8519788
X-RAY DIFFRACTIONf_chiral_restr0.0491031
X-RAY DIFFRACTIONf_plane_restr0.0051251
X-RAY DIFFRACTIONf_dihedral_angle_d14.444247
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.6001-2.6650.32591400.26112598
2.665-2.73690.28941400.24932578
2.7369-2.81720.27991410.24642597
2.8172-2.90790.3251390.24582591
2.9079-3.01140.28461420.23792612
3.0114-3.13160.26511420.22272606
3.1316-3.27350.30111400.21662589
3.2735-3.44530.28941410.20392635
3.4453-3.65990.24561430.17642624
3.6599-3.94050.19121430.15862647
3.9405-4.33340.17561440.13722643
4.3334-4.95210.16371440.12862680
4.9521-6.20790.22651470.16832703
6.2079-19.9780.26631540.18772849

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