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- PDB-1oyg: Crystal structure of Bacillus subtilis levansucrase -

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Basic information

Entry
Database: PDB / ID: 1oyg
TitleCrystal structure of Bacillus subtilis levansucrase
Componentslevansucrase
KeywordsTRANSFERASE / glycoside hydrolase / levansucrase / beta-propeller / levan
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 / SYNCHROTRON / MIR / Resolution: 1.5 Å
AuthorsMeng, G. / Futterer, K.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Structural framework of fructosyl transfer in Bacillus subtilis levansucrase
Authors: Meng, G. / Futterer, K.
History
DepositionApr 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7979
Polymers50,3231
Non-polymers4758
Water6,593366
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.110, 67.014, 123.681
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 50322.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: sacB / Plasmid: pET11c-sacBBs / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05655, levansucrase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal grow
*PLUS
pH: 6.3 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
160 mg/mlprotein11
21 mMdiammonium phosphate12
31 mMsodium acetate12pH6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.18 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 67836 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 9 Å2 / Rsym value: 0.091
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. measured all: 683968 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.58 Å / % possible obs: 98.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.095 / Mean I/σ(I) obs: 7.7

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.96 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.071 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE THERMAL DISPLACEMENT PARAMETERS OF CHAIN A REFLECT THE RESIDUAL B FACTOR AND DOES NOT INCLUDE THE TLS CORRECTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.17508 3386 5 %RANDOM
Rwork0.16499 ---
obs0.1655 64231 98.23 %-
all-64231 --
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: 4.176 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2--0.07 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 29 366 3837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213538
X-RAY DIFFRACTIONr_bond_other_d0.0020.022981
X-RAY DIFFRACTIONr_angle_refined_deg1.0781.9364778
X-RAY DIFFRACTIONr_angle_other_deg0.7336986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2855439
X-RAY DIFFRACTIONr_chiral_restr0.070.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023982
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02705
X-RAY DIFFRACTIONr_nbd_refined0.1970.2597
X-RAY DIFFRACTIONr_nbd_other0.2360.23520
X-RAY DIFFRACTIONr_nbtor_other0.080.21910
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0850.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.221
X-RAY DIFFRACTIONr_mcbond_it0.2911.52178
X-RAY DIFFRACTIONr_mcangle_it0.56723505
X-RAY DIFFRACTIONr_scbond_it1.05931360
X-RAY DIFFRACTIONr_scangle_it1.6564.51273
LS refinement shellResolution: 1.5→1.581 Å / Total num. of bins used: 10
RfactorNum. reflection
Rfree0.167 497
Rwork0.158 9237
obs-9734
Refinement TLS params.Method: refined / Origin x: 44.2858 Å / Origin y: 29.8237 Å / Origin z: 15.2957 Å
111213212223313233
T0.0152 Å20.0118 Å2-0.0042 Å2-0.0105 Å2-0.0091 Å2--0.0274 Å2
L0.4757 °20.0205 °20.0125 °2-0.3416 °20.049 °2--0.5204 °2
S-0.0171 Å °-0.0367 Å °0.0325 Å °0.0294 Å °0.015 Å °0.0067 Å °-0.0391 Å °0.0018 Å °0.0021 Å °
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.175 / Rfactor Rwork: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.006
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.1
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.58 Å

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