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- PDB-2o7i: The X-ray crystal structure of a thermophilic cellobiose binding ... -

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Basic information

Entry
Database: PDB / ID: 2o7i
TitleThe X-ray crystal structure of a thermophilic cellobiose binding protein bound with cellobiose
ComponentsOligopeptide ABC transporter, periplasmic oligopeptide-binding protein
KeywordsSUGAR BINDING PROTEIN / periplasmic binding protein / cellulose / thermophilic proteins / cellobiose binding protein
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / outer membrane-bounded periplasmic space
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-cellobiose / Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCuneo, M.J. / Hellinga, H.W.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural Analysis of Semi-specific Oligosaccharide Recognition by a Cellulose-binding Protein of Thermotoga maritima Reveals Adaptations for Functional Diversification of the Oligopeptide ...Title: Structural Analysis of Semi-specific Oligosaccharide Recognition by a Cellulose-binding Protein of Thermotoga maritima Reveals Adaptations for Functional Diversification of the Oligopeptide Periplasmic Binding Protein Fold.
Authors: Cuneo, M.J. / Beese, L.S. / Hellinga, H.W.
History
DepositionDec 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 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: Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0712
Polymers68,7291
Non-polymers3421
Water9,008500
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.030, 107.030, 118.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2198-

HOH

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Components

#1: Protein Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein


Mass: 68728.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm0031 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Rosetta / References: UniProt: Q9WXN8
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 0.2M Ammonium Sulfate, 30% PEG MME 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 109675 / Num. obs: 109675 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.909 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.8
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.5-1.60.57831029701901399.8
1.6-1.80.3216.621365626629100
1.8-2.20.11216.123075828559100
2.2-2.50.05928.18956211108100
2.5-30.053327946110081100
3-3.60.04239.7462315899100
3.6-40.03448.7173672214100
4-4.50.02856.3139361777100
4.5-50.02657.39029115599.9
5-60.02459.810204132499.9
60.02361.681021080100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1VR5

1vr5


Resolution: 1.5→48.74 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.461 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 5484 5 %RANDOM
Rwork0.192 ---
all0.193 109673 --
obs0.193 109673 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.423 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---0.48 Å20 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4812 0 23 500 5335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225014
X-RAY DIFFRACTIONr_bond_other_d0.0010.023425
X-RAY DIFFRACTIONr_angle_refined_deg1.121.956861
X-RAY DIFFRACTIONr_angle_other_deg0.84238317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3865597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58523.803234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41915777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.891523
X-RAY DIFFRACTIONr_chiral_restr0.0660.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025568
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021077
X-RAY DIFFRACTIONr_nbd_refined0.20.2975
X-RAY DIFFRACTIONr_nbd_other0.1860.23622
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22490
X-RAY DIFFRACTIONr_nbtor_other0.0830.22298
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2359
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.227
X-RAY DIFFRACTIONr_mcbond_it0.6021.53147
X-RAY DIFFRACTIONr_mcbond_other0.1111.51171
X-RAY DIFFRACTIONr_mcangle_it0.8824810
X-RAY DIFFRACTIONr_scbond_it1.29532437
X-RAY DIFFRACTIONr_scangle_it1.7894.52048
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 397 -
Rwork0.29 7555 -
obs-7952 100 %

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