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- PDB-5xsj: XylFII-LytSN complex -

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Basic information

Entry
Database: PDB / ID: 5xsj
TitleXylFII-LytSN complex
Components
  • Periplasmic binding protein/LacI transcriptional regulator
  • Signal transduction histidine kinase, LytS
KeywordsSUGAR BINDING PROTEIN / Two component system / histidine kinase / signal transmission across the membrane / D-xylose uptake
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / carbohydrate binding / membrane
Similarity search - Function
Signal transduction histidine kinase, internal region / : / Histidine kinase / Periplasmic binding protein / Periplasmic binding protein domain / HAMP domain profile. / HAMP domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. ...Signal transduction histidine kinase, internal region / : / Histidine kinase / Periplasmic binding protein / Periplasmic binding protein domain / HAMP domain profile. / HAMP domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Periplasmic binding protein-like I
Similarity search - Domain/homology
beta-D-xylopyranose / Periplasmic binding protein/LacI transcriptional regulator / histidine kinase
Similarity search - Component
Biological speciesClostridium beijerinckii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.202 Å
AuthorsLi, J.X. / Wang, C.Y. / Zhang, P.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670755 China
National Natural Science Foundation of China (NSFC)31322016 China
National Natural Science Foundation of China (NSFC)31630003 China
National Natural Science Foundation of China (NSFC)31421061 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 14, 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 1.2Feb 20, 2019Group: Data collection / 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 / chem_comp ...atom_site / 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 / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 15, 2021Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 2.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Periplasmic binding protein/LacI transcriptional regulator
L: Signal transduction histidine kinase, LytS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7873
Polymers50,6372
Non-polymers1501
Water4,720262
1
X: Periplasmic binding protein/LacI transcriptional regulator
L: Signal transduction histidine kinase, LytS
hetero molecules

X: Periplasmic binding protein/LacI transcriptional regulator
L: Signal transduction histidine kinase, LytS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5746
Polymers101,2744
Non-polymers3002
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area6260 Å2
ΔGint-35 kcal/mol
Surface area32440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.681, 143.688, 87.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11L-369-

HOH

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Components

#1: Protein Periplasmic binding protein/LacI transcriptional regulator


Mass: 33704.441 Da / Num. of mol.: 1 / 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: Protein Signal transduction histidine kinase, LytS


Mass: 16932.582 Da / Num. of mol.: 1 / Fragment: UNP residues 1-134
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_2378 / Production host: Escherichia coli (E. coli) / References: UniProt: A6LW08
#3: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 3.27 Å3/Da / Density % sol: 62.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.2 M lithium sulfate, 2.0 M ammonium sulfate, 0.1 M MES pH 6.6

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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: Apr 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 33221 / % possible obs: 97.87 % / Redundancy: 6.4 % / Net I/σ(I): 14.61

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data collection
HKL-3000data processing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.202→45.182 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 1999 6.02 %
Rwork0.1942 --
obs0.1956 33211 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.202→45.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3066 0 10 262 3338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083122
X-RAY DIFFRACTIONf_angle_d1.0584209
X-RAY DIFFRACTIONf_dihedral_angle_d13.3461172
X-RAY DIFFRACTIONf_chiral_restr0.045493
X-RAY DIFFRACTIONf_plane_restr0.005542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2021-2.25710.23871150.24651792X-RAY DIFFRACTION80
2.2571-2.31810.28391310.24872042X-RAY DIFFRACTION91
2.3181-2.38640.27761430.23942243X-RAY DIFFRACTION100
2.3864-2.46340.25311440.23272244X-RAY DIFFRACTION100
2.4634-2.55140.24891450.23012271X-RAY DIFFRACTION100
2.5514-2.65360.25571450.23112255X-RAY DIFFRACTION100
2.6536-2.77430.2271450.21942259X-RAY DIFFRACTION100
2.7743-2.92050.25621450.22282262X-RAY DIFFRACTION100
2.9205-3.10350.24251450.21662271X-RAY DIFFRACTION100
3.1035-3.3430.24141460.20512271X-RAY DIFFRACTION100
3.343-3.67930.20321460.17412282X-RAY DIFFRACTION100
3.6793-4.21140.16891470.16022296X-RAY DIFFRACTION100
4.2114-5.30460.1741490.15442318X-RAY DIFFRACTION100
5.3046-45.19110.22461530.18712406X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -37.6378 Å / Origin y: -22.8289 Å / Origin z: -15.6264 Å
111213212223313233
T0.2459 Å20.0493 Å20.0252 Å2-0.2545 Å2-0.0133 Å2--0.2608 Å2
L0.8224 °2-0.3386 °20.7417 °2-1.075 °2-0.9945 °2--1.7421 °2
S-0.0387 Å °-0.0467 Å °-0.0362 Å °0.163 Å °0.0928 Å °-0.018 Å °-0.1047 Å °-0.0062 Å °-0.0564 Å °
Refinement TLS groupSelection details: all

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