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- PDB-2b3b: Thermus thermophilus Glucose/Galactose Binding Protein With Bound... -

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Basic information

Entry
Database: PDB / ID: 2b3b
TitleThermus thermophilus Glucose/Galactose Binding Protein With Bound Glucose
Componentsglucose-binding protein
KeywordsSUGAR BINDING PROTEIN / protein-carbohydrate complex / glucose / galactose / periplasmic binding protein
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / beta-D-glucopyranose / alpha-D-glucopyranose / Glucose-binding protein
Function and homology information
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsCuneo, M.J. / Changela, A. / Warren, J.J. / Beese, L.S. / Hellinga, H.W.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The crystal structure of a thermophilic glucose binding protein reveals adaptations that interconvert mono and di-saccharide binding sites.
Authors: Cuneo, M.J. / Changela, A. / Warren, J.J. / Beese, L.S. / Hellinga, H.W.
History
DepositionSep 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._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 1.5Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQEUNCE THE AUTHORS STATE THAT THE DISCREPANCIES BETWEEN GENBANK AND AMINO ACID SEQUENCE IN PDB ...SEQEUNCE THE AUTHORS STATE THAT THE DISCREPANCIES BETWEEN GENBANK AND AMINO ACID SEQUENCE IN PDB ARE DUE TO ERRORS IN THE PUBLISHED SEQUENCE OR ERRORS AS A RESULT OF CLONING THE GENE FOR CRYSTALLIZATION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glucose-binding protein
B: glucose-binding protein
C: glucose-binding protein
D: glucose-binding protein
E: glucose-binding protein
F: glucose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,62812
Polymers264,5476
Non-polymers1,0816
Water34,8951937
1
A: glucose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2712
Polymers44,0911
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: glucose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2712
Polymers44,0911
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: glucose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2712
Polymers44,0911
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: glucose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2712
Polymers44,0911
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: glucose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2712
Polymers44,0911
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: glucose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2712
Polymers44,0911
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.643, 134.874, 159.547
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
glucose-binding protein


Mass: 44091.215 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Species: Thermus thermophilus / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: ttc0328 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Rosetta Gami / References: UniProt: Q72KX2
#2: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1937 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10% (w/v) Isopropanol, 0.1M Sodium Citrate pH5.6, 10% 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: 0.97917 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 181610 / % possible obs: 95.6 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.086 / Χ2: 1.767
Reflection shellResolution: 1.95→2.02 Å / % possible obs: 82.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.4 / Num. measured obs: 15463 / Χ2: 0.818 / % possible all: 82.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
SHELXL-97phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.81 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2.4 / ESU R: 0.175 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 9116 5 %RANDOM
Rwork0.185 ---
all0.187 ---
obs0.186 181451 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.086 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2---0.97 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18208 0 72 1937 20217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02218760
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216903
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.93925501
X-RAY DIFFRACTIONr_angle_other_deg0.847339257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10852345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21724.148810
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.887153022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.41715108
X-RAY DIFFRACTIONr_chiral_restr0.0890.22728
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0220999
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023833
X-RAY DIFFRACTIONr_nbd_refined0.2130.23905
X-RAY DIFFRACTIONr_nbd_other0.1770.216840
X-RAY DIFFRACTIONr_nbtor_refined0.1780.29181
X-RAY DIFFRACTIONr_nbtor_other0.0850.29624
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.21496
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2130.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.232
X-RAY DIFFRACTIONr_mcbond_it0.9521.515002
X-RAY DIFFRACTIONr_mcbond_other0.1671.54828
X-RAY DIFFRACTIONr_mcangle_it1.08218538
X-RAY DIFFRACTIONr_scbond_it1.83738739
X-RAY DIFFRACTIONr_scangle_it2.6234.56963
LS refinement shellResolution: 1.953→2.004 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 607 -
Rwork0.242 10675 -
all-11282 -
obs--81.25 %

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