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- PDB-7bjc: Inulosucrase from Halalkalicoccus jeotgali in complex with sucrose -

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Basic information

Entry
Database: PDB / ID: 7bjc
TitleInulosucrase from Halalkalicoccus jeotgali in complex with sucrose
ComponentsLevansucrase
KeywordsTRANSFERASE / inulosucrase / levansucrase
Function / homologylevansucrase activity / Glycoside hydrolase, family 68 / Levansucrase/Invertase / carbohydrate utilization / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / sucrose / Levansucrase
Function and homology information
Biological speciesHalalkalicoccus jeotgali B3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsGhauri, K. / Pijning, T. / Munawar, N. / Ali, H. / Ghauri, M.A. / Anwar, M.A. / Wallis, R.
CitationJournal: Febs J. / Year: 2021
Title: Crystal structure of an inulosucrase from Halalkalicoccus jeotgali B3T, a halophilic archaeal strain.
Authors: Ghauri, K. / Pijning, T. / Munawar, N. / Ali, H. / Ghauri, M.A. / Anwar, M.A. / Wallis, R.
History
DepositionJan 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc / pdbx_entity_branch_descriptor
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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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
I: Levansucrase
J: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)479,50520
Polymers476,08310
Non-polymers3,42310
Water00
1
A: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9512
Polymers47,6081
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9512
Polymers47,6081
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9512
Polymers47,6081
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9512
Polymers47,6081
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9512
Polymers47,6081
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9512
Polymers47,6081
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9512
Polymers47,6081
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9512
Polymers47,6081
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9512
Polymers47,6081
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9512
Polymers47,6081
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.746, 141.804, 169.318
Angle α, β, γ (deg.)90.000, 97.540, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31(chain C and (resid 9 through 413 or resid 480))
41(chain D and (resid 9 through 413 or resid 480))
51chain E
61(chain F and (resid 9 through 413 or resid 480))
71chain G
81chain H
91(chain I and (resid 9 through 413 or resid 480))
101chain J

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA9 - 413
211chain BB9 - 413
311(chain C and (resid 9 through 413 or resid 480))C0
411(chain D and (resid 9 through 413 or resid 480))D0
511chain EE9 - 413
611(chain F and (resid 9 through 413 or resid 480))F0
711chain GG9 - 413
811chain HH9 - 413
911(chain I and (resid 9 through 413 or resid 480))I0
1011chain JJ9 - 413

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Components

#1: Protein
Levansucrase


Mass: 47608.250 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halalkalicoccus jeotgali B3 (archaea) / Gene: HacjB3_04715, C497_03082 / Production host: Escherichia coli (E. coli) / References: UniProt: D8J9C2
#2: Polysaccharide
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
Has ligand of interestY

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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: 2.94 Å3/Da / Density % sol: 58.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium/sodium tartrate, 0.1 M Bis Tris propane-HCl, pH 7.5 and 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.89 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 3.11→60.6 Å / Num. obs: 76873 / % possible obs: 98 % / Redundancy: 6.8 % / CC1/2: 0.945 / Rpim(I) all: 0.353 / Rrim(I) all: 0.147 / Net I/σ(I): 4.5
Reflection shellResolution: 3.11→3.28 Å / Num. unique obs: 3844 / CC1/2: 0.769 / Rpim(I) all: 0.766 / % possible all: 83

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D47

4d47


Resolution: 3.11→60.6 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2663 3761 4.92 %
Rwork0.2435 72718 -
obs0.2446 76479 77.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.23 Å2 / Biso mean: 55.5557 Å2 / Biso min: 12.36 Å2
Refinement stepCycle: final / Resolution: 3.11→60.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31758 0 230 0 31988
Biso mean--56.79 --
Num. residues----4054
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A19691X-RAY DIFFRACTION11.308TORSIONAL
12B19691X-RAY DIFFRACTION11.308TORSIONAL
13C19691X-RAY DIFFRACTION11.308TORSIONAL
14D19691X-RAY DIFFRACTION11.308TORSIONAL
15E19691X-RAY DIFFRACTION11.308TORSIONAL
16F19691X-RAY DIFFRACTION11.308TORSIONAL
17G19691X-RAY DIFFRACTION11.308TORSIONAL
18H19691X-RAY DIFFRACTION11.308TORSIONAL
19I19691X-RAY DIFFRACTION11.308TORSIONAL
110J19691X-RAY DIFFRACTION11.308TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.11-3.150.3385390.357280384223
3.15-3.190.3805480.359784989724
3.19-3.230.3871420.362793697827
3.23-3.280.3711520.36991041109330
3.28-3.330.3047690.34821230129936
3.33-3.380.3852740.34481390146440
3.38-3.440.3338780.32961620169846
3.44-3.50.3166930.31291815190853
3.5-3.560.35021020.31852211231363
3.56-3.630.34041280.30462552268073
3.63-3.70.34231840.31022962314686
3.7-3.780.31561690.29663303347295
3.78-3.870.2881660.28713451361798
3.87-3.970.29381800.27973403358399
3.97-4.070.3121950.25143467366299
4.07-4.190.29581800.24933463364399
4.19-4.330.25021830.23163418360199
4.33-4.480.24531660.20563460362699
4.48-4.660.24221700.19043461363199
4.66-4.880.22231770.18833473365099
4.88-5.130.21981740.19743484365899
5.13-5.450.25091900.19973447363799
5.45-5.870.2211610.20883486364799
5.87-6.470.21831630.20743497366099
6.47-7.40.22052140.2123456367099
7.4-9.320.18831810.1893510369199
9.32-60.60.211830.21483530371398
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)
12.29351.3461-0.3243.8823-0.50841.33780.33970.51880.16850.1110.42240.0158-0.1636-0.781-0.16730.38830.31250.166-0.5733-0.712-0.12665.81994.064111.4174
22.1084-0.84890.17841.8898-1.3093.46950.43640.1731-0.1749-0.4939-0.069-0.29190.60180.3025-0.20360.37290.06790.05160.1769-0.1250.343530.7168-21.099880.0123
31.2968-0.7968-0.51381.9256-0.48432.4739-0.01050.179-0.1148-0.22130.1958-0.21110.18080.1761-0.09320.1053-0.0631-0.04190.2592-0.11730.302861.663347.716840.9669
41.53980.0508-0.67842.2393-0.34811.60920.1766-0.03820.0793-0.1868-0.0637-0.0823-0.10290.1256-0.08650.33940.03930.11580.1064-0.07160.22373.362117.79975.4869
50.59520.7291-0.51892.9846-0.37584.13050.2842-0.8426-0.11030.112-0.35630.33460.0695-1.15420.158-0.11730.40240.12160.0788-0.36090.304979.8203-3.769680.9041
61.8925-0.31180.05461.9881-0.62852.6402-0.2397-0.11020.46050.08330.0295-0.1877-0.66750.03720.11990.34320.0622-0.07390.17-0.10450.291134.4311-55.087836.4371
71.14422.2690.2272.5132-0.30093.19231.3127-0.45131.43650.0781-0.7892-0.0640.6993-1.5808-0.0644-0.3282-0.1169-0.54711.3908-0.271-0.2476-7.374465.511540.3943
82.19331.02111.28222.6863-0.27934.43080.48870.4831-0.86090.0748-0.0884-0.05280.79850.4189-0.20740.16970.216-0.10350.0927-0.29480.546781.513-29.287940.4727
91.317-0.7881.14872.7531-0.19293.20890.3957-0.4146-0.5671-0.17570.00130.18730.7724-0.7202-0.25960.419-0.1437-0.20.92630.19110.37843.927-29.49390.7318
101.11640.404-0.88852.15960.9261.77740.22710.25520.1920.0953-0.1462-0.1522-0.4413-0.5378-0.07250.36960.32340.11750.6230.08980.264820.91744.677828.1528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 9 through 413)A9 - 413
2X-RAY DIFFRACTION2(chain 'B' and resid 9 through 413)B9 - 413
3X-RAY DIFFRACTION3(chain 'C' and resid 9 through 414)C9 - 414
4X-RAY DIFFRACTION4(chain 'D' and resid 9 through 414)D9 - 414
5X-RAY DIFFRACTION5(chain 'E' and resid 9 through 413)E9 - 413
6X-RAY DIFFRACTION6(chain 'F' and resid 9 through 414)F9 - 414
7X-RAY DIFFRACTION7(chain 'G' and resid 9 through 413)G9 - 413
8X-RAY DIFFRACTION8(chain 'H' and resid 9 through 413)H9 - 413
9X-RAY DIFFRACTION9(chain 'I' and resid 9 through 414)I9 - 414
10X-RAY DIFFRACTION10(chain 'J' and resid 9 through 413)J9 - 413

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