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- PDB-2vk2: Crystal structure of a galactofuranose binding protein -

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Basic information

Entry
Database: PDB / ID: 2vk2
TitleCrystal structure of a galactofuranose binding protein
ComponentsABC TRANSPORTER PERIPLASMIC-BINDING PROTEIN YTFQ
KeywordsTRANSPORT PROTEIN / ABC TRANSPORT / GALACTOFURANOSE / TRANSPORT / PERIPLASM
Function / homology
Function and homology information


hexose import across plasma membrane / galactose transmembrane transport / galactose binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space
Similarity search - Function
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
beta-D-galactofuranose / Galactofuranose-binding protein YtfQ
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsMuller, A. / Horler, R.S.P. / Thomas, G.H. / Wilson, K.S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Furanose-Specific Sugar Transport: Characterization of a Bacterial Galactofuranose-Binding Protein.
Authors: Horler, R.S.P. / Muller, A. / Williamson, D.C. / Potts, J.R. / Wilson, K.S. / Thomas, G.H.
History
DepositionDec 16, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_validate_chiral / struct_ref_seq / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_validate_chiral.auth_atom_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: 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: ABC TRANSPORTER PERIPLASMIC-BINDING PROTEIN YTFQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5562
Polymers33,3761
Non-polymers1801
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.745, 51.535, 116.091
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 ABC TRANSPORTER PERIPLASMIC-BINDING PROTEIN YTFQ / YTFQ


Mass: 33376.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BOUND TO GALACTOFURANOSE / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PET21B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: P39325
#2: Sugar ChemComp-GZL / beta-D-galactofuranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGalfbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactofuranoseCOMMON NAMEGMML 1.0
b-D-GalfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC-TERMINAL HIS-TAG

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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: 2.1 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 6 / Details: MALIC, MES, TRIS, BUFFER SYSTEM PH 6; 25% PEG 1.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9788
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 78867 / % possible obs: 91 % / Observed criterion σ(I): 1.5 / Redundancy: 6.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.5 / % possible all: 39

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DBP

1dbp


Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.336 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 3946 5 %RANDOM
Rwork0.178 ---
obs0.179 74826 91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2--0.19 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 12 366 2599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0222301
X-RAY DIFFRACTIONr_bond_other_d0.0010.021548
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.9833114
X-RAY DIFFRACTIONr_angle_other_deg1.0063.0013826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1165302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.11926.44490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.2415416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.867157
X-RAY DIFFRACTIONr_chiral_restr0.1280.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02399
X-RAY DIFFRACTIONr_nbd_refined0.20.2478
X-RAY DIFFRACTIONr_nbd_other0.1780.21679
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21156
X-RAY DIFFRACTIONr_nbtor_other0.0810.21101
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0770.2277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.080.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1590.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0570.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6611.51585
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05122380
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2173892
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7474.5731
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 94 -
Rwork0.272 2148 -
obs--35.42 %

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