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- PDB-2ioy: Crystal structure of Thermoanaerobacter tengcongensis ribose bind... -

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Basic information

Entry
Database: PDB / ID: 2ioy
TitleCrystal structure of Thermoanaerobacter tengcongensis ribose binding protein
ComponentsPeriplasmic sugar-binding protein
KeywordsSUGAR BINDING PROTEIN / Ribose binding protein / thermophilic proteins
Function / homologyPeriplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / beta-D-ribopyranose / Periplasmic sugar-binding proteins
Function and homology information
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCuneo, M.J. / Hellinga, H.W.
CitationJournal: Bmc Struct.Biol. / Year: 2008
Title: The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog.
Authors: Cuneo, M.J. / Tian, Y. / Allert, M. / Hellinga, H.W.
History
DepositionOct 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 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 21, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic sugar-binding protein
B: Periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8964
Polymers60,5952
Non-polymers3002
Water6,233346
1
A: Periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4482
Polymers30,2981
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4482
Polymers30,2981
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.180, 35.800, 118.030
Angle α, β, γ (deg.)90.00, 107.02, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a monomer

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Components

#1: Protein Periplasmic sugar-binding protein


Mass: 30297.631 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Gene: tte0206 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-BL21 / References: UniProt: Q8RD41
#2: Sugar ChemComp-RIP / beta-D-ribopyranose / beta-D-ribose / D-ribose / ribose / RIBOSE(PYRANOSE FORM) / Ribose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5
IdentifierTypeProgram
DRibpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribopyranoseCOMMON NAMEGMML 1.0
b-D-RibpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal growTemperature: 290 K / pH: 4
Details: 0.1M Na Citrate, pH 4.0, 0.1M Potassium Phosphate Mono-Basic, 50% PEG1000, Micro-batch, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. all: 37592 / Num. obs: 37592 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 7.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 1.9 / Num. measured all: 16732 / Num. unique all: 5405 / Rsym value: 0.324 / % possible all: 95.1

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345data collection
XDSdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.995 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1890 5 %RANDOM
Rwork0.199 ---
all0.201 37592 --
obs0.201 37592 95.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.876 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.26 Å2
2--0.53 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4265 0 20 346 4631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224351
X-RAY DIFFRACTIONr_bond_other_d0.0010.022896
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.9835908
X-RAY DIFFRACTIONr_angle_other_deg0.92837235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0485598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34827.528178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41915816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5451510
X-RAY DIFFRACTIONr_chiral_restr0.1260.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024963
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02723
X-RAY DIFFRACTIONr_nbd_refined0.2110.2954
X-RAY DIFFRACTIONr_nbd_other0.1810.23029
X-RAY DIFFRACTIONr_nbtor_refined0.1650.22207
X-RAY DIFFRACTIONr_nbtor_other0.0840.22249
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.219
X-RAY DIFFRACTIONr_mcbond_it0.7991.53131
X-RAY DIFFRACTIONr_mcbond_other0.1561.51168
X-RAY DIFFRACTIONr_mcangle_it1.16324611
X-RAY DIFFRACTIONr_scbond_it1.97831590
X-RAY DIFFRACTIONr_scangle_it2.9144.51291
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 140 -
Rwork0.26 2537 -
obs-2677 94.33 %

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