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- PDB-3byl: Crystal structure of B. subtilis levansucrase mutant E342A -

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Basic information

Entry
Database: PDB / ID: 3byl
TitleCrystal structure of B. subtilis levansucrase mutant E342A
ComponentsLevansucrase
KeywordsTRANSFERASE / beta propeller / Glycosyltransferase / Secreted
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 domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsFutterer, K. / Meng, G.
CitationJournal: To be Published
Title: Donor substrate recognition in the raffinose-bound E342A mutant of fructosyltransferase Bacillus subtilis levansucrase
Authors: Meng, G. / Futterer, K.
History
DepositionJan 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Levansucrase


Theoretical massNumber of molelcules
Total (without water)52,9751
Polymers52,9751
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.133, 67.281, 123.622
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Levansucrase / Beta-D-fructofuranosyl transferase / Sucrose 6-fructosyl transferase


Mass: 52974.766 Da / Num. of mol.: 1 / Mutation: E342A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: SACB / Plasmid: pET11c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05655, levansucrase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.01 Å3/Da / Density % sol: 38.72 %
Crystal growTemperature: 291 K / Method: microdialysis / pH: 6.3
Details: diammonium phosphate, sodium acetate, pH 6.3, MICRODIALYSIS, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Mar 3, 2003
RadiationMonochromator: OSCMIC CONFOCAL MIRROR OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.07→30 Å / Num. all: 26368 / Num. obs: 26368 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 25
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.068 / Mean I/σ(I) obs: 25.1 / Rsym value: 0.068 / % possible all: 98.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OYG

1oyg


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.171 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1286 5.1 %RANDOM
Rwork0.18 ---
all0.182 25331 --
obs0.182 25331 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.689 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2--0.75 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3438 0 0 266 3704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213513
X-RAY DIFFRACTIONr_bond_other_d0.0020.022980
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.9334759
X-RAY DIFFRACTIONr_angle_other_deg0.77136982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7955439
X-RAY DIFFRACTIONr_chiral_restr0.0770.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023978
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02705
X-RAY DIFFRACTIONr_nbd_refined0.1930.2607
X-RAY DIFFRACTIONr_nbd_other0.2380.23403
X-RAY DIFFRACTIONr_nbtor_other0.0810.21880
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2260
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3180.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.219
X-RAY DIFFRACTIONr_mcbond_it0.3411.52178
X-RAY DIFFRACTIONr_mcangle_it0.6223504
X-RAY DIFFRACTIONr_scbond_it1.15531335
X-RAY DIFFRACTIONr_scangle_it1.7774.51255
LS refinement shellResolution: 2.1→2.213 Å / Total num. of bins used: 10
RfactorNum. reflection
Rfree0.223 177
Rwork0.176 3449
obs-3626
Refinement TLS params.Method: refined / Origin x: 44.3369 Å / Origin y: 29.8527 Å / Origin z: 15.2939 Å
111213212223313233
T0.0192 Å20.0107 Å2-0.008 Å2-0.0065 Å2-0.0009 Å2--0.0266 Å2
L0.5544 °20.0314 °20.0183 °2-0.4787 °20.1491 °2--0.6473 °2
S-0.0096 Å °-0.0351 Å °0.0374 Å °0.0312 Å °0.009 Å °0.0021 Å °-0.0334 Å °0.0097 Å °0.0007 Å °
Refinement TLS groupSelection: ALL

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