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

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Basic information

Entry
Database: PDB / ID: 6rkj
TitleThe crystal structure of AbnE, an arabino-oligosaccharide binding protein, in complex with arabinooctaose
ComponentsArabino-oligosaccharids-binding protein
KeywordsSUGAR BINDING PROTEIN / Geobacillus stearothermophilus / arabino-oligosaccharide / arabinohexaose / ABC transporter
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: 1.601 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
Water12,520695
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-7 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.477, 95.608, 120.076
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.: 695 / 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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 60551 / % possible obs: 99.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 10.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4532 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RKH

6rkh


Resolution: 1.601→34.912 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.03
RfactorNum. reflection% reflection
Rfree0.1877 2932 4.85 %
Rwork0.1588 --
obs0.1603 60472 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.601→34.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3341 0 68 695 4104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063638
X-RAY DIFFRACTIONf_angle_d1.1444967
X-RAY DIFFRACTIONf_dihedral_angle_d14.1261427
X-RAY DIFFRACTIONf_chiral_restr0.047534
X-RAY DIFFRACTIONf_plane_restr0.005635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6014-1.62760.24261200.21212491X-RAY DIFFRACTION92
1.6276-1.65570.22811460.19832647X-RAY DIFFRACTION98
1.6557-1.68580.20511420.18222686X-RAY DIFFRACTION99
1.6858-1.71820.21121360.17052724X-RAY DIFFRACTION100
1.7182-1.75330.18061160.16462713X-RAY DIFFRACTION100
1.7533-1.79140.18331520.17112754X-RAY DIFFRACTION100
1.7914-1.83310.20681340.1642679X-RAY DIFFRACTION100
1.8331-1.87890.20111450.16962776X-RAY DIFFRACTION100
1.8789-1.92970.20271310.16252665X-RAY DIFFRACTION100
1.9297-1.98650.21841390.16852755X-RAY DIFFRACTION100
1.9865-2.05060.17571420.15982714X-RAY DIFFRACTION100
2.0506-2.12390.19811490.16222745X-RAY DIFFRACTION100
2.1239-2.20890.20311470.16112746X-RAY DIFFRACTION100
2.2089-2.30940.20961300.15992767X-RAY DIFFRACTION100
2.3094-2.43110.18711620.16192728X-RAY DIFFRACTION100
2.4311-2.58340.18531390.16382756X-RAY DIFFRACTION100
2.5834-2.78280.20881330.16482779X-RAY DIFFRACTION100
2.7828-3.06270.19621260.16432797X-RAY DIFFRACTION100
3.0627-3.50550.19021500.15262791X-RAY DIFFRACTION100
3.5055-4.41520.14871470.13422850X-RAY DIFFRACTION100
4.4152-34.92070.16041460.14642977X-RAY DIFFRACTION100

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