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- PDB-5xss: XylFII molecule -

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Basic information

Entry
Database: PDB / ID: 5xss
TitleXylFII molecule
ComponentsPeriplasmic binding protein/LacI transcriptional regulator
KeywordsSUGAR BINDING PROTEIN / Two component system / histidine kinase / signal transmission across the membrane / D-xylose uptake
Function / homologyPeriplasmic binding protein / Periplasmic binding protein domain / Periplasmic binding protein-like I / carbohydrate binding / beta-D-xylopyranose / Periplasmic binding protein/LacI transcriptional regulator
Function and homology information
Biological speciesClostridium beijerinckii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.093 Å
AuthorsLi, J.X. / Wang, C.Y. / Zhang, P.
Funding support China, 5items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31670755 China
the National Natural Science Foundation of China31322016 China
the National Natural Science Foundation of China31630003 China
the National Natural Science Foundation of China31421061 China
the Chinese Academy of SciencesQYZDB-SSW-SMC006 China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Molecular mechanism of environmental d-xylose perception by a XylFII-LytS complex in bacteria
Authors: Li, J. / Wang, C. / Yang, G. / Sun, Z. / Guo, H. / Shao, K. / Gu, Y. / Jiang, W. / Zhang, P.
History
DepositionJun 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 15, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 27, 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
X: Periplasmic binding protein/LacI transcriptional regulator
A: Periplasmic binding protein/LacI transcriptional regulator
B: Periplasmic binding protein/LacI transcriptional regulator
C: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,8358
Polymers139,2344
Non-polymers6014
Water14,700816
1
X: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9592
Polymers34,8091
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-3 kcal/mol
Surface area11720 Å2
MethodPISA
2
A: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9592
Polymers34,8091
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-5 kcal/mol
Surface area11920 Å2
MethodPISA
3
B: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9592
Polymers34,8091
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-4 kcal/mol
Surface area12020 Å2
MethodPISA
4
C: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9592
Polymers34,8091
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-4 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.541, 68.059, 76.677
Angle α, β, γ (deg.)89.89, 65.15, 87.33
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Periplasmic binding protein/LacI transcriptional regulator


Mass: 34808.508 Da / Num. of mol.: 4 / Fragment: UNP residues 25-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052) (bacteria)
Strain: ATCC 51743 / NCIMB 8052 / Gene: Cbei_2377 / Production host: Escherichia coli (E. coli) / References: UniProt: A6LW07
#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.: 4
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
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.: 816 / 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: 46.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 20% Polyethylene glycol 8000, 0.1 M phosphate-citrate pH 4.2, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9798 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.093→50 Å / Num. obs: 70577 / % possible obs: 96.77 % / Redundancy: 3.8 % / Net I/σ(I): 15.8
Reflection shellResolution: 2.0933→2.1208 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 7.8 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data processing
PHENIXphasing
RefinementResolution: 2.093→30.782 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.89
RfactorNum. reflection% reflection
Rfree0.2144 3572 5.06 %
Rwork0.1804 --
obs0.1821 70577 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.093→30.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8295 0 40 816 9151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118407
X-RAY DIFFRACTIONf_angle_d1.32211318
X-RAY DIFFRACTIONf_dihedral_angle_d13.8013180
X-RAY DIFFRACTIONf_chiral_restr0.0651359
X-RAY DIFFRACTIONf_plane_restr0.0051446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0933-2.12080.22841200.18272223X-RAY DIFFRACTION83
2.1208-2.14990.2351430.1892536X-RAY DIFFRACTION97
2.1499-2.18060.22891410.19572677X-RAY DIFFRACTION97
2.1806-2.21310.22621450.19872502X-RAY DIFFRACTION97
2.2131-2.24770.2681310.19872644X-RAY DIFFRACTION97
2.2477-2.28450.21831220.19682580X-RAY DIFFRACTION97
2.2845-2.32390.24451370.19412621X-RAY DIFFRACTION98
2.3239-2.36620.241330.19352573X-RAY DIFFRACTION97
2.3662-2.41160.25161400.19782613X-RAY DIFFRACTION98
2.4116-2.46080.25231560.19372589X-RAY DIFFRACTION98
2.4608-2.51430.23051430.19352634X-RAY DIFFRACTION98
2.5143-2.57280.25761210.1932609X-RAY DIFFRACTION98
2.5728-2.63710.21551500.1852581X-RAY DIFFRACTION98
2.6371-2.70840.21371620.18522625X-RAY DIFFRACTION98
2.7084-2.7880.21751250.18892592X-RAY DIFFRACTION98
2.788-2.87790.23941350.18692616X-RAY DIFFRACTION98
2.8779-2.98070.18391590.18422594X-RAY DIFFRACTION98
2.9807-3.09990.21691420.18382665X-RAY DIFFRACTION98
3.0999-3.24090.22621400.18562619X-RAY DIFFRACTION99
3.2409-3.41150.22551250.17182615X-RAY DIFFRACTION98
3.4115-3.6250.18261620.16592597X-RAY DIFFRACTION98
3.625-3.90440.18151300.16512598X-RAY DIFFRACTION97
3.9044-4.29630.18831290.15322554X-RAY DIFFRACTION96
4.2963-4.91580.17991190.15312510X-RAY DIFFRACTION94
4.9158-6.18520.22451310.18552581X-RAY DIFFRACTION96
6.1852-30.78520.20681310.18682457X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: -58.9476 Å / Origin y: 24.3419 Å / Origin z: -2.2899 Å
111213212223313233
T0.1181 Å20.0029 Å2-0.0183 Å2-0.1004 Å2-0.0015 Å2--0.1116 Å2
L0.3527 °2-0.0134 °2-0.2151 °2-0.0564 °2-0.0153 °2--0.2653 °2
S0.0156 Å °-0.0036 Å °-0.0185 Å °0.0016 Å °-0.0142 Å °0.0004 Å °-0.0572 Å °-0.0012 Å °-0.0016 Å °
Refinement TLS groupSelection details: all

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