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- PDB-5um2: Functional and structural characterization of a Sulfate-binding p... -

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Basic information

Entry
Database: PDB / ID: 5um2
TitleFunctional and structural characterization of a Sulfate-binding protein (Sbp) from Xanthomonas citri
ComponentsABC transporter sulfate binding protein
KeywordsTRANSPORT PROTEIN / ABC transporter / periplasmic domain
Function / homology
Function and homology information


sulfur compound binding / ABC-type sulfate transporter activity
Similarity search - Function
Sulphate/thiosulphate-binding site / Prokaryotic sulfate-binding proteins signature 2. / Thiosulphate/Sulfate-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ABC transporter sulfate binding protein
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsPereira, C.T. / Hyvonen, M. / Balan, A.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/16094-4 Brazil
Sao Paulo Research Foundation (FAPESP)2015/14514-1 Brazil
Citation
Journal: Mol. Plant Microbe Interact. / Year: 2017
Title: Sulfate-Binding Protein (Sbp) from Xanthomonas citri: Structure and Functional Insights.
Authors: Pereira, C.T. / Roesler, C. / Faria, J.N. / Fessel, M.R. / Balan, A.
#1: Journal: BMC Genomics / Year: 2015
Title: The sulfur/sulfonates transport systems in Xanthomonas citri pv. citri.
Authors: Pereira, C.T. / Moutran, A. / Fessel, M. / Balan, A.
History
DepositionJan 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _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: ABC transporter sulfate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7484
Polymers37,4641
Non-polymers2843
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-33 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.060, 54.540, 34.200
Angle α, β, γ (deg.)90.00, 98.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-569-

HOH

21A-694-

HOH

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Components

#1: Protein ABC transporter sulfate binding protein


Mass: 37464.090 Da / Num. of mol.: 1 / Fragment: residues 25-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: sbp, XAC1017 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8PNN7
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.39 Å3/Da / Density % sol: 48.53 % / Description: rod crystals
Crystal growTemperature: 291.2 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Potassium Sulfate, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.14→30.16 Å / Num. obs: 207316 / % possible obs: 93.04 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.025 / Net I/σ(I): 15.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
PHENIX(1.11.1_2575: ???)model building
PDB_EXTRACT3.22data extraction
XDS3.3data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SBP

1sbp


Resolution: 1.14→30.158 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 13.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1389 5595 4.97 %
Rwork0.1207 --
obs0.1217 112639 93.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.14→30.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 16 295 2819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092648
X-RAY DIFFRACTIONf_angle_d1.0373610
X-RAY DIFFRACTIONf_dihedral_angle_d17.744971
X-RAY DIFFRACTIONf_chiral_restr0.087384
X-RAY DIFFRACTIONf_plane_restr0.009477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.1530.27511200.25512491X-RAY DIFFRACTION65
1.153-1.16650.27611400.24672776X-RAY DIFFRACTION73
1.1665-1.18080.25981700.24053175X-RAY DIFFRACTION83
1.1808-1.19570.23341740.22763271X-RAY DIFFRACTION87
1.1957-1.21140.22941820.21253427X-RAY DIFFRACTION89
1.2114-1.2280.21011840.19763404X-RAY DIFFRACTION90
1.228-1.24560.21351680.18623430X-RAY DIFFRACTION90
1.2456-1.26420.21061670.16923561X-RAY DIFFRACTION92
1.2642-1.28390.21561880.1653504X-RAY DIFFRACTION93
1.2839-1.3050.17351870.14923612X-RAY DIFFRACTION94
1.305-1.32750.1591990.12263650X-RAY DIFFRACTION95
1.3275-1.35160.15752140.11573542X-RAY DIFFRACTION95
1.3516-1.37760.1321830.10213701X-RAY DIFFRACTION95
1.3776-1.40570.11951840.10213648X-RAY DIFFRACTION96
1.4057-1.43630.13721960.09793695X-RAY DIFFRACTION96
1.4363-1.46970.12531660.09953697X-RAY DIFFRACTION96
1.4697-1.50650.13511880.09473698X-RAY DIFFRACTION96
1.5065-1.54720.12491700.08973699X-RAY DIFFRACTION96
1.5472-1.59270.10621910.08333687X-RAY DIFFRACTION97
1.5927-1.64410.10351990.08543713X-RAY DIFFRACTION97
1.6441-1.70290.11611960.08923743X-RAY DIFFRACTION97
1.7029-1.7710.11722000.0923687X-RAY DIFFRACTION97
1.771-1.85160.12022140.09773730X-RAY DIFFRACTION98
1.8516-1.94920.12681720.10593815X-RAY DIFFRACTION98
1.9492-2.07130.12431840.10923739X-RAY DIFFRACTION98
2.0713-2.23120.12062080.11083788X-RAY DIFFRACTION98
2.2312-2.45570.13222050.11323763X-RAY DIFFRACTION98
2.4557-2.81080.15222060.1233772X-RAY DIFFRACTION98
2.8108-3.54040.13242100.13043797X-RAY DIFFRACTION98
3.5404-30.16870.13912300.12883829X-RAY DIFFRACTION97

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