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- PDB-3i5o: The X-ray crystal structure of a thermophilic cellobiose binding ... -

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Basic information

Entry
Database: PDB / ID: 3i5o
TitleThe X-ray crystal structure of a thermophilic cellobiose binding protein bound with cellopentaose
ComponentsOligopeptide ABC transporter, periplasmic oligopeptide-binding protein
KeywordsSUGAR BINDING PROTEIN / cellulose / carbohydrate-binding protein / periplasmic binding protein / cellopentaose
Function / homology
Function and homology information


peptide transmembrane transporter activity / peptide transport / outer membrane-bounded periplasmic space / metal ion binding
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-cellopentaose / 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
DepositionJul 6, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionJul 21, 2009ID: 2O7J
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 22, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / 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 / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
B: Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,1154
Polymers137,4572
Non-polymers1,6572
Water15,979887
1
A: Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5572
Polymers68,7291
Non-polymers8291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5572
Polymers68,7291
Non-polymers8291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.110, 101.460, 108.290
Angle α, β, γ (deg.)90.000, 94.070, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 2 - 583 / Label seq-ID: 4 - 585

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 2:583 )AA
2chain B and (resseq 2:583 )BB

NCS oper: (Code: given
Matrix: (-0.988763, -0.024936, -0.1474), (0.026092, -0.999642, -0.005917), (-0.147199, -0.009696, 0.989059)
Vector: 58.5578, 64.881599, 58.8339)
DetailsThe biological unit is a single polypeptide chain. There are two biological units in the deposited files.

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Components

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


Mass: 68728.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm0031, TM_0031 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q9WXN8
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellopentaose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellopentaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 887 / 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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M NaCacodylate, pH 6.5, 0.2M Magnesium acetate, 20% PEG 4000, 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 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 6, 2006
RadiationMonochromator: Si 111 / Protocol: 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: 205603 / Num. obs: 205603 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.456 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.7
Reflection shellResolution: 1.5→1.6 Å / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 4 / Num. measured obs: 93763 / Num. unique obs: 31437 / % possible all: 83.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O7I

2o7i


Resolution: 1.5→48.67 Å / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.802 / SU ML: 0.01 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.225 10324 5.02 %Random
Rwork0.204 ---
obs0.205 205555 96.24 %-
all-205555 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.652 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso max: 71.44 Å2 / Biso mean: 23.436 Å2 / Biso min: 9 Å2
Baniso -1Baniso -2Baniso -3
1--8.968 Å20 Å20.373 Å2
2--12.333 Å20 Å2
3----10.354 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9529 0 112 887 10528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510134
X-RAY DIFFRACTIONf_angle_d1.07313868
X-RAY DIFFRACTIONf_chiral_restr0.0681433
X-RAY DIFFRACTIONf_plane_restr0.0051758
X-RAY DIFFRACTIONf_dihedral_angle_d17.733622
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4666X-RAY DIFFRACTIONPOSITIONAL0.027
12B4666X-RAY DIFFRACTIONPOSITIONAL0.027
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.5170.3632830.3514779506271
1.517-1.5350.3782680.3395179544777
1.535-1.5540.3533160.3225533584982
1.554-1.5730.3272960.3056044634090
1.573-1.5940.3023190.2796492681196
1.594-1.6160.3013690.2646542691198
1.616-1.6390.2853320.2496665699798
1.639-1.6630.2793320.2456592692498
1.663-1.6890.2583670.2236638700598
1.689-1.7170.2323260.226659698598
1.717-1.7470.2444000.2186593699398
1.747-1.7780.2473730.2096654702799
1.778-1.8130.2323600.2046640700099
1.813-1.850.2273420.2076617695999
1.85-1.890.2313650.2016714707999
1.89-1.9340.2293700.2026627699799
1.934-1.9820.2373650.2026711707699
1.982-2.0360.2293190.2056670698999
2.036-2.0960.2433940.2076651704599
2.096-2.1630.2133190.1976755707499
2.163-2.2410.2493760.2016683705999
2.241-2.330.2183140.1986751706599
2.33-2.4360.2273600.2016705706599
2.436-2.5650.2363360.1976739707599
2.565-2.7260.2233540.2056766712099
2.726-2.9360.2183860.2076698708499
2.936-3.2310.223510.2066768711999
3.231-3.6990.23490.1936776712599
3.699-4.660.1693440.15767877131100
4.66-48.6950.1683390.1676803714298

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