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- PDB-3c6q: Apo and ligand-bound form of a thermophilic glucose/xylose bindin... -

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Basic information

Entry
Database: PDB / ID: 3c6q
TitleApo and ligand-bound form of a thermophilic glucose/xylose binding protein
ComponentsSugar ABC transporter, periplasmic sugar-binding protein
KeywordsSUGAR BINDING PROTEIN / glucose binding protein / xylose binding protein / periplasmic binding protein / glucose / xylose
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / carbohydrate binding
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-xylopyranose / Sugar ABC transporter, periplasmic sugar-binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsCuneo, M.J. / Hellinga, H.W.
CitationJournal: To be Published
Title: Open to closed transition of a thermophilic glucose binding protein
Authors: Cuneo, M.J. / Hellinga, H.W.
History
DepositionFeb 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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 / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Sugar ABC transporter, periplasmic sugar-binding protein
A: Sugar ABC transporter, periplasmic sugar-binding protein
C: Sugar ABC transporter, periplasmic sugar-binding protein
D: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,1286
Polymers134,8284
Non-polymers3002
Water6,215345
1
B: Sugar ABC transporter, periplasmic sugar-binding protein


Theoretical massNumber of molelcules
Total (without water)33,7071
Polymers33,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sugar ABC transporter, periplasmic sugar-binding protein


Theoretical massNumber of molelcules
Total (without water)33,7071
Polymers33,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8572
Polymers33,7071
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8572
Polymers33,7071
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.100, 75.750, 100.520
Angle α, β, γ (deg.)90.000, 89.900, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999999, 0.000372, -0.001637), (0.000372, -1, 0.000139), (-0.001637, -0.00014, -0.999999)40.567001, 0.431856, 50.215801
3given(0.999994, 0.001311, -0.003345), (0.001314, -0.999999, 0.000745), (-0.003344, -0.000749, -0.999994)40.692101, -75.280701, 50.115398
DetailsThe biolgical assembly is a monomeric protein consisting of a single polypeptide chain. In this structure there are two forms, one of which has xylose bound, the other does not.

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Components

#1: Protein
Sugar ABC transporter, periplasmic sugar-binding protein


Mass: 33706.934 Da / Num. of mol.: 4 / Fragment: UNP residues 32-335 / Mutation: E41C, E163C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0114 / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9WXW9
#2: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose / Xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1M HEPES, 23% PEG 10000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 11.86 / Number: 172271 / Rmerge(I) obs: 0.098 / D res high: 2.3 Å / Num. obs: 53176 / % possible obs: 97.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
620306196.510.02
4.56422199.710.037
3.24.51292899.610.075
33.2422999.310.2
2.73899199.110.277
2.52.7861598.810.289
2.42.5538898.410.278
2.32.4574389.310.273
ReflectionResolution: 2.3→20 Å / Num. obs: 53176 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.874 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.86
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 4.3 / Num. measured obs: 16111 / Num. unique all: 16111 / Num. unique obs: 5743 / % possible all: 89.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
PHASERphasing
RefinementStarting model: PDB entry 2H3H

2h3h


Resolution: 2.3→19.868 Å / FOM work R set: 0.753 / Stereochemistry target values: ml
RfactorNum. reflection% reflection
Rfree0.281 2659 5 %
Rwork0.214 --
obs-53174 98.24 %
Solvent computationBsol: 17.196 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso max: 131.39 Å2 / Biso mean: 39.56 Å2 / Biso min: 4.03 Å2
Baniso -1Baniso -2Baniso -3
1-3.267 Å20 Å20.057 Å2
2--0.318 Å2-0 Å2
3----3.585 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9198 0 20 345 9563
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d1.021
X-RAY DIFFRACTIONf_bond_d0.0071
X-RAY DIFFRACTIONf_chiral_restr0.0631
X-RAY DIFFRACTIONf_dihedral_angle_d17.8021
X-RAY DIFFRACTIONf_plane_restr0.0041
X-RAY DIFFRACTIONf_nbd_refined4.1071
LS refinement shellResolution: 2.3→2.3093 Å /
RfactorNum. reflection
Rwork0.4041 -
obs-183

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