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

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Basic information

Entry
Database: PDB / ID: 6rkl
TitleThe crystal structure of AbnE, an arabino-oligosaccharide binding protein, in complex with arabinoheptaose
ComponentsArabino-oligosaccharids-binding protein
KeywordsSUGAR BINDING PROTEIN / Geobacillus stearothermophilus / ABC transporter / arabino-oligosaccharide / arabinohexaose
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 / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionApr 30, 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)49,7255
Polymers48,6901
Non-polymers1,0354
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-8 kcal/mol
Surface area18290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.248, 95.542, 120.014
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-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose


Type: oligosaccharide / Mass: 810.704 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-5LArafa1-5LArafa1-5LArafa1-5LArafa1-5LArafa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a211h-1a_1-4]/1-1-1-1-1-1/a5-b1_b5-c1_c5-d1_d5-e1_e5-f1WURCSPDB2Glycan 1.1.0
[][a-L-Araf]{[(5+1)][a-L-Araf]{[(5+1)][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.: 518 / 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: 2.38 Å3/Da / Density % sol: 48.33 %
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: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 35228 / % possible obs: 99.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2 / Num. unique obs: 4737 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RKH

6rkh


Resolution: 2→28.625 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.59
RfactorNum. reflection% reflection
Rfree0.1953 1762 5 %
Rwork0.1633 --
obs0.1649 35228 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→28.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3341 0 68 518 3927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083560
X-RAY DIFFRACTIONf_angle_d1.1574842
X-RAY DIFFRACTIONf_dihedral_angle_d14.5231367
X-RAY DIFFRACTIONf_chiral_restr0.048518
X-RAY DIFFRACTIONf_plane_restr0.005618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8955-1.94670.2865820.25561624X-RAY DIFFRACTION61
1.9467-2.0040.24721340.23362309X-RAY DIFFRACTION88
2.004-2.06870.27071270.20062576X-RAY DIFFRACTION97
2.0687-2.14260.26131250.17892642X-RAY DIFFRACTION100
2.1426-2.22830.211640.18062617X-RAY DIFFRACTION100
2.2283-2.32970.21651500.17232672X-RAY DIFFRACTION100
2.3297-2.45250.22631500.17042646X-RAY DIFFRACTION100
2.4525-2.6060.22151170.17212687X-RAY DIFFRACTION100
2.606-2.80710.20821410.1712689X-RAY DIFFRACTION100
2.8071-3.08930.2211460.16982660X-RAY DIFFRACTION100
3.0893-3.53560.17671390.15752725X-RAY DIFFRACTION100
3.5356-4.45180.16151490.13882723X-RAY DIFFRACTION100
4.4518-28.62850.14461380.1422896X-RAY DIFFRACTION100

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