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- PDB-6rl2: The crystal structure of AbnE, an arabino-oligosaccharide binding... -

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Basic information

Entry
Database: PDB / ID: 6rl2
TitleThe crystal structure of AbnE, an arabino-oligosaccharide binding protein, in complex with arabinotetraose
ComponentsArabino-oligosaccharids-binding protein
KeywordsSUGAR BINDING PROTEIN / ABC transporter / arabino-oligosaccharide / Geobacillus stearothermophilus / arabinotetraose
Function / homology: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / Arabino-oligosaccharids-binding protein
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsLansky, S. / Salama, R. / Shoham, Y. / Shoham, G.
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Carbohydrate-Binding Capability and Functional Conformational Changes of AbnE, an Arabino-oligosaccharide Binding Protein.
Authors: Lansky, S. / Salama, R. / Shulami, S. / Lavid, N. / Sen, S. / Schapiro, I. / Shoham, Y. / Shoham, G.
History
DepositionMay 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arabino-oligosaccharids-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4615
Polymers48,6901
Non-polymers7714
Water6,666370
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-10 kcal/mol
Surface area18160 Å2
Unit cell
Length a, b, c (Å)96.787, 120.031, 39.641
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Arabino-oligosaccharids-binding protein


Mass: 48689.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: abnE / Production host: Escherichia coli (E. coli) / References: UniProt: B3EYM9
#2: Polysaccharide alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L- ...alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose


Type: oligosaccharide / Mass: 546.474 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-5LArafa1-5LArafa1-5LArafa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a211h-1a_1-4]/1-1-1-1/a5-b1_b5-c1_c5-d1WURCSPDB2Glycan 1.1.0
[][a-L-Araf]{[(5+1)][a-L-Araf]{[(5+1)][a-L-Araf]{[(5+1)][a-L-Araf]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 22% PEG 4K, 0.1M Tris/HCl buffer, pH 9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.94→48.39 Å / Num. obs: 40538 / % possible obs: 99 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 24.7
Reflection shellResolution: 1.94→2.06 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 5211 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RKH

6rkh


Resolution: 1.94→44.883 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.44
RfactorNum. reflection% reflection
Rfree0.2154 2025 5 %
Rwork0.1722 --
obs0.1744 40512 94.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.94→44.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 50 370 3758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083505
X-RAY DIFFRACTIONf_angle_d1.1024761
X-RAY DIFFRACTIONf_dihedral_angle_d14.0981328
X-RAY DIFFRACTIONf_chiral_restr0.046507
X-RAY DIFFRACTIONf_plane_restr0.005608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8141-1.85940.401970.33241850X-RAY DIFFRACTION65
1.8594-1.90970.38081160.28352201X-RAY DIFFRACTION77
1.9097-1.96590.28651310.24242490X-RAY DIFFRACTION87
1.9659-2.02930.25951450.20252749X-RAY DIFFRACTION97
2.0293-2.10190.27541520.20352886X-RAY DIFFRACTION100
2.1019-2.1860.22121510.19012869X-RAY DIFFRACTION100
2.186-2.28550.23581500.1842860X-RAY DIFFRACTION100
2.2855-2.4060.20921520.18272877X-RAY DIFFRACTION100
2.406-2.55670.2441520.1852895X-RAY DIFFRACTION100
2.5567-2.75410.22621530.18312900X-RAY DIFFRACTION100
2.7541-3.03120.20981530.17862915X-RAY DIFFRACTION100
3.0312-3.46970.23941540.17152919X-RAY DIFFRACTION100
3.4697-4.37090.17581570.13922977X-RAY DIFFRACTION100
4.3709-44.89670.17011620.14263099X-RAY DIFFRACTION99

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