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- PDB-1w18: Crystal Structure of levansucrase from Gluconacetobacter diazotro... -

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Basic information

Entry
Database: PDB / ID: 1w18
TitleCrystal Structure of levansucrase from Gluconacetobacter diazotrophicus
ComponentsLEVANSUCRASE
KeywordsTRANSFERASE / FRUCTOSYL TRANSFERASE / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


levansucrase / levansucrase activity / carbohydrate utilization / extracellular region
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 speciesGLUCONACETOBACTER DIAZOTROPHICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMartinez-Fleites, C. / Ortiz-Lombardia, M. / Pons, T. / Tarbouriech, N. / Taylor, E.J. / Hernandez, L. / Davies, G.J.
CitationJournal: Biochem.J. / Year: 2005
Title: Crystal Structure of Levansucrase from the Gram- Negative Bacterium Gluconacetobacter Diazotrophicus.
Authors: Martinez-Fleites, C. / Ortiz-Lombardia, M. / Pons, T. / Tarbouriech, N. / Taylor, E.J. / Arrieta, J.G. / Hernandez, L. / Davies, G.J.
History
DepositionJun 16, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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

Downloads & links

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Assembly

Deposited unit
A: LEVANSUCRASE
B: LEVANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,3396
Polymers107,9542
Non-polymers3844
Water3,477193
1
A: LEVANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1693
Polymers53,9771
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: LEVANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1693
Polymers53,9771
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.803, 119.391, 215.101
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99944, 0.03243, 0.0077), (0.03222, -0.88086, -0.47228), (-0.00853, 0.47227, -0.88141)
Vector: -7.77629, 140.43097, 200.68687)

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Components

#1: Protein LEVANSUCRASE / BETA-D-FRUCTOFURANOSYL TRANSFERASE / SUCROSE 6-FRUCTOSYL TRANSFERASE


Mass: 53977.125 Da / Num. of mol.: 2 / Fragment: RESIDUES 62-554 / Source method: isolated from a natural source
Source: (natural) GLUCONACETOBACTER DIAZOTROPHICUS (bacteria)
Strain: SRT4 / References: UniProt: Q43998, levansucrase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 58.4 %
Crystal growpH: 5.6
Details: 0.5M AS, 30% ETHANOL, 0.1M NA-CITRATE PH5.6, pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→51.98 Å / Num. obs: 48568 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0001refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OYG

1oyg


Resolution: 2.5→105.41 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.907 / SU B: 21.154 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.368 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2444 5 %RANDOM
Rwork0.197 ---
obs0.2 46069 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.33 Å2
Baniso -1Baniso -2Baniso -3
1--2.06 Å20 Å20 Å2
2--4.57 Å20 Å2
3----2.51 Å2
Refinement stepCycle: LAST / Resolution: 2.5→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7635 0 20 193 7848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0217883
X-RAY DIFFRACTIONr_bond_other_d0.0010.026641
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.90110781
X-RAY DIFFRACTIONr_angle_other_deg0.886315417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6565983
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55524.078412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.132151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6441548
X-RAY DIFFRACTIONr_chiral_restr0.0890.21119
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029155
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021723
X-RAY DIFFRACTIONr_nbd_refined0.2090.21835
X-RAY DIFFRACTIONr_nbd_other0.20.27277
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.24604
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2327
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.280.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6121.56129
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.78627861
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.23233540
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.924.52920
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: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.388 172
Rwork0.291 3354
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)
12.43920.09490.91861.7494-0.16862.02420.00340.32710.4923-0.33380.11540.14950.02070.1503-0.11880.0676-0.0239-0.0428-0.02220.12750.101626.60147.89895.19
21.9521-0.3063-1.32531.0307-0.47152.4528-0.1007-0.08360.00980.18340.15160.0498-0.1481-0.1984-0.05090.0818-0.04280.09040.4855-0.1702-0.049621.02556.397149.106
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 550
2X-RAY DIFFRACTION2B1 - 550

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