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- PDB-5ocp: The periplasmic binding protein component of the arabinose ABC tr... -

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Basic information

Entry
Database: PDB / ID: 5ocp
TitleThe periplasmic binding protein component of the arabinose ABC transporter from Shewanella sp. ANA-3 bound to alpha and beta-L-arabinofuranose
ComponentsPeriplasmic binding protein/LacI transcriptional regulator
KeywordsSUGAR BINDING PROTEIN / ABC transporter / periplasmic / binding protein / arabinose / arabinofuranose
Function / homology
Function and homology information


Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / alpha-L-arabinofuranose / beta-L-arabinofuranose / Periplasmic binding protein/LacI transcriptional regulator
Similarity search - Component
Biological speciesShewanella sp. ANA-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHerman, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N01040X/1 United Kingdom
CitationJournal: To Be Published
Title: CHARACTERISATION OF A FURANOSE SPECIFIC ABC TRANSPORTER ESSENTIAL FOR ARABINOSE UTILISATION FROM THE LIGNOCELLULOSE DEGRADING BACTERIUM SHEWANELLA SP. ANA-3
Authors: Herman, R. / Drousiotis, K. / Wilkinson, A.J. / Thomas, G.H.
History
DepositionJul 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 2.0Dec 19, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.label_alt_id / _pdbx_nonpoly_scheme.ndb_seq_num
Revision 3.0Jul 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_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic binding protein/LacI transcriptional regulator
B: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,01015
Polymers65,6142
Non-polymers1,39613
Water8,305461
1
A: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6609
Polymers32,8071
Non-polymers8538
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3506
Polymers32,8071
Non-polymers5435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.917, 86.327, 87.282
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Periplasmic binding protein/LacI transcriptional regulator / ABC transporter periplasmic-binding protein / GafA


Mass: 32806.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Amino acids 1 to 291 make up the protein in the periplasm. Amino acids 292 to 302 are part of a His-tag used for purification.
Source: (gene. exp.) Shewanella sp. ANA-3 (bacteria) / Gene: Shewana3_2073 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: A0KWY4

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Sugars , 2 types, 4 molecules

#3: Sugar ChemComp-AHR / alpha-L-arabinofuranose / alpha-L-arabinose / L-arabinose / arabinose / Arabinose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LArafaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-arabinofuranoseCOMMON NAMEGMML 1.0
a-L-ArafIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-FUB / beta-L-arabinofuranose / beta-L-arabinose / L-arabinose / arabinose / Arabinose


Type: L-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LArafbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-arabinofuranoseCOMMON NAMEGMML 1.0
b-L-ArafIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 470 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium Nitrate, pH 6.2, 20 % PEG 3,350

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→43.64 Å / Num. obs: 62122 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.032 / Rrim(I) all: 0.088 / Net I/σ(I): 3.77
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.597 / CC1/2: 0.903 / Rpim(I) all: 0.237 / Rrim(I) all: 0.643 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VK2

2vk2


Resolution: 1.7→43.64 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.159 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.105
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 3081 5 %RANDOM
Rwork0.1669 ---
obs0.1687 58975 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 109.37 Å2 / Biso mean: 23.716 Å2 / Biso min: 8.99 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å2-0 Å2-0 Å2
2--1.91 Å20 Å2
3----0.74 Å2
Refinement stepCycle: final / Resolution: 1.7→43.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4618 0 92 461 5171
Biso mean--38.9 34.86 -
Num. residues----604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194762
X-RAY DIFFRACTIONr_bond_other_d0.0020.024458
X-RAY DIFFRACTIONr_angle_refined_deg2.0341.9586414
X-RAY DIFFRACTIONr_angle_other_deg1.086310357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.185596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6625.209215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61115809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6311524
X-RAY DIFFRACTIONr_chiral_restr0.1310.2727
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025271
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02905
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 231 -
Rwork0.218 4272 -
all-4503 -
obs--99.73 %

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