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- PDB-4d47: X-ray structure of the levansucrase from Erwinia amylovora -

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Basic information

Entry
Database: PDB / ID: 4d47
TitleX-ray structure of the levansucrase from Erwinia amylovora
ComponentsLEVANSUCRASE
KeywordsTRANSFERASE / GLYCOSIDE HYDROLASE FAMILY 68 / SUCROSE HYDROLYSIS / FIVE- BLADED BETA-PROPELLER / FIRE BLIGHT
Function / homology
Function and homology information


levansucrase / levansucrase activity / carbohydrate utilization
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
beta-D-fructofuranose / alpha-D-glucopyranose / Levansucrase / :
Similarity search - Component
Biological speciesERWINIA AMYLOVORA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsWuerges, J. / Caputi, L. / Cianci, M. / Benini, S.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: The Crystal Structure of Erwinia Amylovora Levansucrase Provides a Snapshot of the Products of Sucrose Hydrolysis Trapped Into the Active Site.
Authors: Wuerges, J. / Caputi, L. / Cianci, M. / Boivin, S. / Meijers, R. / Benini, S.
History
DepositionOct 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEVANSUCRASE
B: LEVANSUCRASE
C: LEVANSUCRASE
D: LEVANSUCRASE
E: LEVANSUCRASE
F: LEVANSUCRASE
G: LEVANSUCRASE
H: LEVANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)374,60024
Polymers371,7178
Non-polymers2,88216
Water1,71195
1
A: LEVANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8253
Polymers46,4651
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LEVANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8253
Polymers46,4651
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LEVANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8253
Polymers46,4651
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LEVANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8253
Polymers46,4651
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: LEVANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8253
Polymers46,4651
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: LEVANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8253
Polymers46,4651
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: LEVANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8253
Polymers46,4651
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: LEVANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8253
Polymers46,4651
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)155.589, 178.736, 158.806
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.8548, -0.5013, 0.1339), (-0.5076, 0.7543, -0.4165), (0.1078, -0.424, -0.8992)298.5, 113.6, 115.8
2given(0.835, -0.5298, 0.1486), (-0.5425, -0.7478, 0.3828), (-0.0917, -0.4002, -0.9118)5.082, 164.1, 148.8
3given(-0.4388, 0.7874, -0.4328), (-0.7965, -0.1178, 0.5931), (0.416, 0.605, 0.6789)227.5, 172.6, -89.46
4given(-0.8341, -0.5309, -0.15), (0.5435, -0.7441, -0.3885), (0.09467, -0.4056, 0.9092)302.1, 9.026, 45.06
5given(0.4387, 0.7838, 0.4395), (0.796, -0.1119, -0.5949), (-0.4171, 0.6108, -0.673)43.26, -52.53, 106.2
6given(0.8515, -0.5065, -0.1357), (0.5131, 0.7514, 0.415), (-0.1082, -0.4229, 0.8997)17.9, -93.75, 81.26
7given(-1, 0.000844, -2.3E-5), (0.000844, 1, -0.001345), (2.1E-5, -0.001345, -1)341.6, -0.1454, 79.46

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Components

#1: Protein
LEVANSUCRASE


Mass: 46464.641 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: HYDROLYSIS PRODUCTS FRUCTOSE AND GLUCOSE ARE PRESENT AT THE ACTIVE SITE
Source: (gene. exp.) ERWINIA AMYLOVORA (bacteria) / Strain: EA273 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D4IGH9, UniProt: A0A0M3KKU6*PLUS, levansucrase
#2: Sugar
ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsFRUCTOSE (FRU): FRUCTOSE IS PART OF THE HYDROLYSIS PRODUCT OF THE SUBSTRATE SUCROSE ALPHA-D-GLUCOSE ...FRUCTOSE (FRU): FRUCTOSE IS PART OF THE HYDROLYSIS PRODUCT OF THE SUBSTRATE SUCROSE ALPHA-D-GLUCOSE (GLC): GLUCOSE IS PART OF THE HYDROLYSIS PRODUCT OF THE SUBSTRATE SUCROSE

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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: 2.98 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growDetails: 0.1 M POTASSIUM THIOCYANATE, 30% W/V PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.968
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.77→178.74 Å / Num. obs: 112787 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 6 % / Biso Wilson estimate: 30.79 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 3
Reflection shellResolution: 2.77→2.92 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W18

1w18


Resolution: 2.77→20.851 Å / SU ML: 0.4 / σ(F): 1.36 / Phase error: 36.3 / Stereochemistry target values: ML
Details: N-TERMINAL RESIDUES 1-3 AND THE C- -TERMINAL RESIDUE 415 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2978 5626 5 %
Rwork0.262 --
obs0.2638 112243 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.138 Å2
Refinement stepCycle: LAST / Resolution: 2.77→20.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25976 0 192 95 26263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00426918
X-RAY DIFFRACTIONf_angle_d0.95836731
X-RAY DIFFRACTIONf_dihedral_angle_d14.3069677
X-RAY DIFFRACTIONf_chiral_restr0.0363946
X-RAY DIFFRACTIONf_plane_restr0.0044779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.80140.34592070.31153497X-RAY DIFFRACTION100
2.8014-2.83430.36352080.3073499X-RAY DIFFRACTION100
2.8343-2.86880.36421790.30953487X-RAY DIFFRACTION100
2.8688-2.9050.36541870.30843553X-RAY DIFFRACTION100
2.905-2.94310.36081900.30383529X-RAY DIFFRACTION100
2.9431-2.98330.36091710.30543517X-RAY DIFFRACTION100
2.9833-3.02580.38991860.2973540X-RAY DIFFRACTION100
3.0258-3.07080.36611600.30063537X-RAY DIFFRACTION100
3.0708-3.11870.33161760.30293557X-RAY DIFFRACTION99
3.1187-3.16960.32612020.29773494X-RAY DIFFRACTION100
3.1696-3.22410.34671770.29043519X-RAY DIFFRACTION100
3.2241-3.28250.32641650.28673543X-RAY DIFFRACTION100
3.2825-3.34540.28621450.28263568X-RAY DIFFRACTION100
3.3454-3.41340.34331950.27633525X-RAY DIFFRACTION100
3.4134-3.48730.31582030.26673519X-RAY DIFFRACTION100
3.4873-3.5680.31961630.26213598X-RAY DIFFRACTION100
3.568-3.65680.31581980.27193504X-RAY DIFFRACTION100
3.6568-3.75510.28552030.2593536X-RAY DIFFRACTION100
3.7551-3.86490.27341980.24853524X-RAY DIFFRACTION100
3.8649-3.98880.25791950.24933557X-RAY DIFFRACTION100
3.9888-4.13030.26671900.24543570X-RAY DIFFRACTION100
4.1303-4.29430.2632120.23253530X-RAY DIFFRACTION100
4.2943-4.48790.26542020.2163550X-RAY DIFFRACTION100
4.4879-4.72190.24281810.21293592X-RAY DIFFRACTION100
4.7219-5.01390.25371940.21643560X-RAY DIFFRACTION99
5.0139-5.39480.24961750.22463605X-RAY DIFFRACTION100
5.3948-5.92640.24532010.24033594X-RAY DIFFRACTION100
5.9264-6.75830.29352040.25323612X-RAY DIFFRACTION100
6.7583-8.42040.25611870.25743638X-RAY DIFFRACTION99
8.4204-20.85160.31161720.27083763X-RAY DIFFRACTION98
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)
11.2794-0.0495-0.47970.3451-0.16730.72550.00850.0299-0.0908-0.0256-0.0160.05790.0595-0.0468-0.00390.1902-0.0033-0.02120.0982-0.0430.1798159.515329.445521.2322
21.1110.247-0.24810.5553-0.10011.3601-0.0105-0.2273-0.04040.08360.0134-0.08420.05640.0421-0.0020.20070.0453-0.04310.2021-0.02250.1897182.112629.409658.193
30.8302-0.09950.70080.9146-0.20441.62450.1255-0.1592-0.18990.05330.02560.08170.1794-0.1229-0.13920.1407-0.0386-0.00150.19570.02360.2138112.40543.192622.0111
41.1378-0.22020.80140.77060.10571.6616-0.00650.4072-0.2134-0.11020.0505-0.10010.10580.3597-0.04570.2603-0.0233-0.00950.4379-0.1150.3074229.215743.17657.3755
51.4852-0.0523-0.88890.58980.49362.1709-0.1135-0.0407-0.26760.0642-0.03110.15220.3118-0.13480.12450.2411-0.02880.03470.2048-0.01430.2644136.027419.277171.2934
61.35460.2374-0.45630.4726-0.21021.74710.0299-0.0718-0.1046-0.0171-0.0749-0.07140.18960.36990.03380.17440.08530.00470.2398-0.00440.229205.539219.12448.0908
71.36090.21770.74050.8561-0.41721.2052-0.0219-0.13940.17220.104-0.0223-0.0024-0.1321-0.09180.01280.17220.02470.0180.1233-0.06790.2422146.185970.353544.5897
81.6977-0.23730.57880.74320.51171.2031-0.44420.52020.5895-0.29430.14920.1401-0.58470.28850.23080.6173-0.1779-0.24130.33850.14940.4845195.369870.436134.989
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'H' AND (RESID 50 THROUGH 414 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 50 THROUGH 414 )
3X-RAY DIFFRACTION3CHAIN 'E' AND (RESID 50 THROUGH 414 )
4X-RAY DIFFRACTION4CHAIN 'C' AND (RESID 50 THROUGH 414 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 50 THROUGH 414 )
6X-RAY DIFFRACTION6CHAIN 'G' AND (RESID 50 THROUGH 414 )
7X-RAY DIFFRACTION7CHAIN 'F' AND (RESID 50 THROUGH 414 )
8X-RAY DIFFRACTION8CHAIN 'D' AND (RESID 50 THROUGH 414 )

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