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- PDB-4jsd: The X-ray crystal structure of a thermophilic cellobiose binding ... -

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Basic information

Entry
Database: PDB / ID: 4jsd
TitleThe X-ray crystal structure of a thermophilic cellobiose binding protein bound with laminaribiose
ComponentsOligopeptide ABC transporter, periplasmic oligopeptide-binding protein
KeywordsSUGAR BINDING PROTEIN / PERIPLASMIC BINDING PROTEIN / THERMOPHILIC PROTEIN / CELLULOSE / CELLOBIOSE BINDING PROTEIN
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-laminaribiose / Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMunshi, P. / Cuneo, M.J.
CitationJournal: Bmc Struct.Biol. / Year: 2013
Title: Molecular details of ligand selectivity determinants in a promiscuous beta-glucan periplasmic binding protein.
Authors: Munshi, P. / Stanley, C.B. / Ghimire-Rijal, S. / Lu, X. / Myles, D.A. / Cuneo, M.J.
History
DepositionMar 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
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 / 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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)67,7923
Polymers67,4101
Non-polymers3822
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.641, 89.596, 108.245
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 Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein


Mass: 67410.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM0031, TM_0031 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL / References: UniProt: Q9WXN8
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-laminaribiose
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: tmCBP was concentrated to 20 mg/mL and dialyzed into 10 mM Tris, 40 mM NaCl, 0.5 mM TCEP for crystallization. Laminaribiose or laminaripentaose was added to a final concentration of 1 mM ...Details: tmCBP was concentrated to 20 mg/mL and dialyzed into 10 mM Tris, 40 mM NaCl, 0.5 mM TCEP for crystallization. Laminaribiose or laminaripentaose was added to a final concentration of 1 mM prior to crystallization trials. Crystals were grown in drops containing 2 uL of the protein solution mixed with 2 uL of 0.2-0.3 M magnesium acetate or calcium acetate, 20-30% (wt/vol) PEG 3350 equilibrated against 900 uL of the same solution, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 30, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 34613 / Num. obs: 34549 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.037 / Net I/σ(I): 15.4
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3399 / Rsym value: 0.377 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O7I

2o7i


Resolution: 2.05→47.876 Å / SU ML: 0.2 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 2000 5.79 %RANDOM
Rwork0.1837 ---
obs0.1849 34549 97.88 %-
all-34613 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→47.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4780 0 24 293 5097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075031
X-RAY DIFFRACTIONf_angle_d1.7566879
X-RAY DIFFRACTIONf_dihedral_angle_d14.6481820
X-RAY DIFFRACTIONf_chiral_restr0.081700
X-RAY DIFFRACTIONf_plane_restr0.009879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10160.32741380.28022242X-RAY DIFFRACTION96
2.1016-2.15840.31381400.2532283X-RAY DIFFRACTION98
2.1584-2.22190.23751410.23862292X-RAY DIFFRACTION98
2.2219-2.29360.24821410.22612311X-RAY DIFFRACTION98
2.2936-2.37560.22861430.21862318X-RAY DIFFRACTION98
2.3756-2.47070.23251420.21192298X-RAY DIFFRACTION98
2.4707-2.58310.24491410.20892302X-RAY DIFFRACTION98
2.5831-2.71930.28581420.22642303X-RAY DIFFRACTION98
2.7193-2.88960.25651430.20662340X-RAY DIFFRACTION99
2.8896-3.11270.24861450.2132355X-RAY DIFFRACTION99
3.1127-3.42590.20311450.18592352X-RAY DIFFRACTION99
3.4259-3.92140.16231440.16152366X-RAY DIFFRACTION98
3.9214-4.93980.14411460.13392361X-RAY DIFFRACTION97
4.9398-47.88930.15341490.14442426X-RAY DIFFRACTION95

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