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- PDB-2vdt: Crystallographic structure of Levansucrase from Bacillus subtilis... -

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Basic information

Entry
Database: PDB / ID: 2vdt
TitleCrystallographic structure of Levansucrase from Bacillus subtilis mutant S164A
ComponentsLEVANSUCRASE
KeywordsTRANSFERASE / BETA-PROPELLER / GLYCOSYLTRANSFERASE / GLYCOSIDE HYDROLASE / LEVAN / SECRETED / LEVANSUCRASE
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 / Resolution: 3.2 Å
AuthorsOrtiz-Soto, M.E. / Rivera, M. / Rudino-Pinera, E. / Olvera, C. / Lopez-Munguia, A.
CitationJournal: Protein Eng.Des.Sel. / Year: 2008
Title: Selected Mutations in Bacillus Subtilis Levansucrase Semi-Conserved Regions Affecting its Biochemical Properties
Authors: Ortiz-Soto, M.E. / Rivera, M. / Rudino-Pinera, E. / Olvera, C. / Lopez-Munguia, A.
History
DepositionOct 11, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2018Group: Data collection / Database references / Category: citation / Item: _citation.page_last
Revision 1.4Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LEVANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4552
Polymers49,4151
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.880, 55.800, 124.600
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: 49414.594 Da / Num. of mol.: 1 / Fragment: RESIDUES 34-472 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PET 22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P05655, levansucrase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Sequence detailsMUTATION AT RESIDUE 164 FROM SER TO ALA

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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: 1.86 Å3/Da / Density % sol: 31.97 % / Description: NONE
Crystal growMethod: microdialysis / pH: 7
Details: CRYSTALS WERE OBTAINED AFTER 12 DAYS OF MICRODIALYSIS OF THE PURIFIED PROTEIN (8 G/L) AGAINST DEIONIZED WATER., pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200H / Wavelength: 1.5418
DetectorType: RIGAKU-MSC / Detector: IMAGE PLATE / Date: Mar 13, 2007 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→39.41 Å / Num. obs: 5627 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 70.72 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.8 / % possible all: 94.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OYG

1oyg


Resolution: 3.2→39.41 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.297 287 4.6 %RANDOM
Rwork0.2645 ---
obs0.2645 5605 89.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.1 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 62.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.541 Å20 Å20 Å2
2---2.108 Å20 Å2
3---1.567 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.8 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 3.2→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 1 0 3485
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.461.5
X-RAY DIFFRACTIONc_mcangle_it3.912
X-RAY DIFFRACTIONc_scbond_it5.692
X-RAY DIFFRACTIONc_scangle_it7.292.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.43 56 5.9 %
Rwork0.368 892 -
obs--93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP

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