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- PDB-2yfr: Crystal structure of inulosucrase from Lactobacillus johnsonii NCC533 -

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Basic information

Entry
Database: PDB / ID: 2yfr
TitleCrystal structure of inulosucrase from Lactobacillus johnsonii NCC533
ComponentsLEVANSUCRASE
KeywordsTRANSFERASE / FRUCTOSYLTRANSFERASE / GLYCOSIDE HYDROLASE FAMILY GH68 / SUGAR UTILIZATION
Function / homology
Function and homology information


inulosucrase / inulosucrase activity / 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 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Inulosucrase
Similarity search - Component
Biological speciesLACTOBACILLUS JOHNSONII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPijning, T. / Anwar, M.A. / Leemhuis, H. / Kralj, S. / Dijkhuizen, L. / Dijkstra, B.W.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal Structure of Inulosucrase from Lactobacillus: Insights Into the Substrate Specificity and Product Specificity of Gh68 Fructansucrases.
Authors: Pijning, T. / Anwar, M.A. / Boger, M. / Dobruchowska, J.M. / Leemhuis, H. / Kralj, S. / Dijkhuizen, L. / Dijkstra, B.W.
History
DepositionApr 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references
Revision 1.2Dec 20, 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 / struct_site
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 / _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)65,79924
Polymers63,8531
Non-polymers1,94623
Water9,278515
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: LEVANSUCRASE
hetero molecules

A: LEVANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,59948
Polymers127,7072
Non-polymers3,89246
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area12430 Å2
ΔGint-234.8 kcal/mol
Surface area37340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.007, 172.007, 114.581
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LEVANSUCRASE / INULOSUCRASE


Mass: 63853.359 Da / Num. of mol.: 1 / Fragment: RESIDUES 145-708
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOBACILLUS JOHNSONII (bacteria) / Strain: NCC533 / Plasmid: PETINUJ / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q74K42, inulosucrase

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Non-polymers , 6 types, 538 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 3.44 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growpH: 6 / Details: 2 M (NH4)2)SO4, 5% (V/V) 2-PROPANOL, pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.935
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.935 Å / Relative weight: 1
ReflectionResolution: 1.75→41.76 Å / Num. obs: 85480 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.7
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.2 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OYG

1oyg


Resolution: 1.75→121.63 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.201 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 145-175 ARE NOT VISIBLE IN ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.16958 4012 5 %RANDOM
Rwork0.15095 ---
obs0.15189 75901 93.01 %-
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: 25.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.75→121.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4197 0 113 515 4825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224486
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9526121
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0735566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0726.089225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.39715725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.0341512
X-RAY DIFFRACTIONr_chiral_restr0.10.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213458
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6191.52705
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17324371
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.04831781
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3824.51733
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 302 -
Rwork0.223 5578 -
obs--93.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5007-0.36120.95886.0091.26038.6270.2606-0.5219-0.30460.5574-0.20360.3171.1572-0.7699-0.0570.2614-0.236-0.02230.27780.08780.114620.486633.245952.0222
21.90380.4018-0.04310.6450.0160.7296-0.0146-0.106-0.01320.0230.00130.07120.1442-0.18630.01330.1278-0.0609-0.00740.1482-0.02490.081633.665247.450944.3624
30.54020.07890.06950.72230.28490.4364-0.01310.02230.06-0.0377-0.00720.025-0.0489-0.00750.02030.1417-0.0096-0.00460.119-0.01040.119654.904975.965442.5747
41.12970.3641-0.21891.4673-0.04720.8290.0144-0.02930.09050.0393-0.08250.1221-0.033-0.10.06810.10830.006-0.01480.1159-0.04360.138540.251176.742245.5341
50.7120.35960.02271.4522-0.29780.5990.0188-0.16150.03440.0471-0.02920.16520.0666-0.13170.01040.0617-0.02490.00730.1738-0.04110.085431.502557.467148.3662
60.74320.1391-0.05720.72380.24450.451-0.0380.03230.0326-0.0809-0.01570.0556-0.0094-0.08860.05380.1431-0.0182-0.01410.163-0.03240.135345.172558.698138.5168
70.54690.14010.37970.76950.03621.1609-0.03430.0878-0.0383-0.10550.0271-0.0234-0.02390.0350.00720.112-0.01070.00060.1233-0.03350.095256.859162.964232.6336
81.85750.0994-0.57212.3905-0.78482.6428-0.0158-0.0246-0.3295-0.0355-0.02810.00240.29920.05770.04390.11420.0079-0.00890.1116-0.03280.170264.864348.128142.2029
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A176 - 200
2X-RAY DIFFRACTION2A201 - 238
3X-RAY DIFFRACTION3A239 - 367
4X-RAY DIFFRACTION4A368 - 447
5X-RAY DIFFRACTION5A448 - 518
6X-RAY DIFFRACTION6A519 - 611
7X-RAY DIFFRACTION7A612 - 671
8X-RAY DIFFRACTION8A672 - 708

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