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- PDB-7bj4: Inulosucrase from Halalkalicoccus jeotgali bound to kestose -

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Basic information

Entry
Database: PDB / ID: 7bj4
TitleInulosucrase from Halalkalicoccus jeotgali bound to kestose
ComponentsLevansucrase
KeywordsTRANSFERASE / inulosucrase / levansucrase
Function / homologylevansucrase activity / Glycoside hydrolase, family 68 / Levansucrase/Invertase / carbohydrate utilization / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / 1-kestose / Levansucrase
Function and homology information
Biological speciesHalalkalicoccus jeotgali B3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 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 / struct_ncs_dom_lim
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id ..._diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)481,12720
Polymers476,08310
Non-polymers5,04410
Water1,45981
1
A: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1132
Polymers47,6081
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1132
Polymers47,6081
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1132
Polymers47,6081
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1132
Polymers47,6081
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1132
Polymers47,6081
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1132
Polymers47,6081
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1132
Polymers47,6081
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1132
Polymers47,6081
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1132
Polymers47,6081
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1132
Polymers47,6081
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.299, 142.969, 172.870
Angle α, β, γ (deg.)90.000, 98.640, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain H
91chain I
101chain J

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 9 - 414 / Label seq-ID: 9 - 414

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD
5chain EEE
6chain FFF
7chain GGG
8chain HHH
9chain III
10chain JJJ

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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)-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: 1-kestose
DescriptorTypeProgram
DFrufb2-1DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][ha122h-2b_2-5]/1-2-2/a1-b2_b1-c2WURCSPDB2Glycan 1.1.0
[][<C12O10>]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
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: 3.14 Å3/Da / Density % sol: 60.81 %
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: 0.976 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: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.72→106.54 Å / Num. obs: 93379 / % possible obs: 99.2 % / Redundancy: 7 % / CC1/2: 0.991 / Rpim(I) all: 0.097 / Net I/σ(I): 7.7
Reflection shellResolution: 2.72→2.82 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4668 / CC1/2: 0.446 / % possible all: 73.5

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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: 2.72→106.54 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 4744 5.09 %
Rwork0.1973 88457 -
obs0.1988 93201 59.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.14 Å2 / Biso mean: 62.5341 Å2 / Biso min: 26.57 Å2
Refinement stepCycle: final / Resolution: 2.72→106.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31800 0 340 81 32221
Biso mean--53.66 46.14 -
Num. residues----4060
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A19586X-RAY DIFFRACTION11.281TORSIONAL
12B19586X-RAY DIFFRACTION11.281TORSIONAL
13C19586X-RAY DIFFRACTION11.281TORSIONAL
14D19586X-RAY DIFFRACTION11.281TORSIONAL
15E19586X-RAY DIFFRACTION11.281TORSIONAL
16F19586X-RAY DIFFRACTION11.281TORSIONAL
17G19586X-RAY DIFFRACTION11.281TORSIONAL
18H19586X-RAY DIFFRACTION11.281TORSIONAL
19I19586X-RAY DIFFRACTION11.281TORSIONAL
110J19586X-RAY DIFFRACTION11.281TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.72-2.750.485790.368961052
2.75-2.780.593190.41891801894
2.78-2.820.46220.35653033256
2.82-2.850.3478280.34823633917
2.85-2.890.2358270.32124224499
2.89-2.930.2983330.354850854110
2.93-2.970.2795340.324662065413
2.97-3.020.2924470.309976080715
3.02-3.060.3611480.312490295018
3.06-3.110.3587580.31551130118823
3.11-3.170.3561760.31161380145628
3.17-3.220.3441280.29341640176834
3.22-3.290.30131220.2742181230344
3.29-3.350.32521260.27642612273852
3.35-3.430.31991960.26513365356167
3.43-3.510.29212100.25924032424281
3.51-3.590.31342690.25684750501996
3.59-3.690.32111910.28243318350967
3.69-3.80.24492540.22214949520399
3.8-3.920.23932710.19964981525299
3.92-4.060.21722420.18624962520499
4.06-4.220.20532640.16784990525499
4.22-4.420.19942320.15854990522299
4.42-4.650.14662660.14444976524299
4.65-4.940.19672350.148650255260100
4.94-5.320.17342630.163149885251100
5.32-5.860.19962400.182750275267100
5.86-6.710.23562950.199249695264100
6.71-8.450.19072620.184850455307100
8.45-106.540.20162870.19524993528097
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)
11.85330.1159-0.10762.3415-0.11222.1620.00950.10470.0728-0.09190.01920.1665-0.0433-0.0076-00.41350.0582-0.01190.3827-0.03390.37416.3864.83512.308
22.03-0.41520.54662.2363-1.44073.57630.37030.4287-0.1489-0.7422-0.4086-0.25721.03310.841500.83040.35060.02550.6991-0.01420.5962-29.391-21.56181.143
31.6606-0.39850.15672.6741-0.16972.74520.01580.2059-0.0401-0.086-0.0165-0.07540.04690.0193-00.3139-0.0615-0.05010.4626-0.07320.50922.847.6941.192
41.7371-0.0325-0.28021.890.09872.0260.1596-0.02680.0427-0.085-0.1011-0.08650.00310.19100.352-0.00870.01390.2982-0.02940.3908-57.57617.76876.306
51.57950.4120.34472.5525-0.2073.2685-0.1048-0.07950.14560.046-0.00280.3702-0.199-0.3427-00.2710.08630.02110.3456-0.02260.491622.057-4.66982.074
62.11190.0925-0.20171.8852-0.18872.3051-0.0526-0.10820.28260.20720.0121-0.0934-0.3440.0945-00.47320.0406-0.02590.4865-0.11840.468-24.193-55.18535.068
72.92751.43480.33372.83250.31653.09310.2771-0.71540.33460.2995-0.23850.43930.0385-0.703-00.44690.08090.08370.9338-0.06150.5206-67.73166.88140.299
82.0139-0.0830.56662.0155-0.58374.88240.26080.1859-0.4145-0.4079-0.1742-0.01581.42740.2966-00.88690.1313-0.07090.3688-0.02450.569822.049-30.72941.037
91.9953-0.16790.83992.3703-0.22513.51190.2635-0.1488-0.5104-0.09370.11640.19230.7231-0.391100.5563-0.0369-0.14260.71190.05870.6326-55.457-30.111.025
101.70030.02890.03311.56710.04882.12980.03450.00990.14510.0771-0.0361-0.0522-0.212-0.11300.46880.14830.0190.51430.01480.4216-39.3155.68129.416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 30:414 )A30 - 414
2X-RAY DIFFRACTION2( CHAIN B AND RESID 30:414 )B30 - 414
3X-RAY DIFFRACTION3( CHAIN C AND RESID 30:414 )C30 - 414
4X-RAY DIFFRACTION4( CHAIN D AND RESID 30:414 )D30 - 414
5X-RAY DIFFRACTION5( CHAIN E AND RESID 30:414 )E30 - 414
6X-RAY DIFFRACTION6( CHAIN F AND RESID 30:414 )F30 - 414
7X-RAY DIFFRACTION7( CHAIN G AND RESID 30:414 )G30 - 414
8X-RAY DIFFRACTION8( CHAIN H AND RESID 30:414 )H30 - 414
9X-RAY DIFFRACTION9( CHAIN I AND RESID 30:414 )I30 - 414
10X-RAY DIFFRACTION10( CHAIN J AND RESID 30:414 )J30 - 414

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