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- PDB-3ksx: The alkanesulfonate-binding protein SsuA from Xanthomonas axonopo... -

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Basic information

Entry
Database: PDB / ID: 3ksx
TitleThe alkanesulfonate-binding protein SsuA from Xanthomonas axonopodis pv. citri bound to MOPS
ComponentsNitrate transport protein
KeywordsTRANSPORT PROTEIN / SsuA / alkanesulfonate-binding protein / periplasmic-binding protein
Function / homology
Function and homology information


ATPase-coupled transmembrane transporter activity / periplasmic space / membrane
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #20 / Aliphatic sulfonates-binding protein / SsuA/THI5-like / NMT1/THI5 like / Helicase, Ruva Protein; domain 3 / Bacterial periplasmic substrate-binding proteins / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / Helix non-globular / Special ...Helicase, Ruva Protein; domain 3 - #20 / Aliphatic sulfonates-binding protein / SsuA/THI5-like / NMT1/THI5 like / Helicase, Ruva Protein; domain 3 / Bacterial periplasmic substrate-binding proteins / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / Helix non-globular / Special / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Nitrate transport protein
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsBalan, A. / Araujo, F.T. / Barbosa, J.A.R.G.
CitationJournal: To be Published
Title: The crystallographic structure of the SsuA protein reveals how alkanesulfonates enter into the cell
Authors: Balan, A. / Araujo, F.T. / Barbosa, J.A.R.G.
History
DepositionNov 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrate transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0645
Polymers34,5671
Non-polymers4974
Water3,783210
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.042, 86.446, 47.015
Angle α, β, γ (deg.)90.00, 97.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nitrate transport protein


Mass: 34566.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: ssuA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PHQ1
#2: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 1.81 Å3/Da / Density % sol: 32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.2 M MOPS pH 6.8, 0.1 M NaCl, 1.6 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.46 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.46 Å / Relative weight: 1
ReflectionResolution: 1.7→26.14 Å / Num. obs: 26985 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1 % / Rmerge(I) obs: 0.1625 / Net I/σ(I): 9.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1 % / % possible all: 96.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.03 Å26.14 Å
Translation2.03 Å26.14 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E4R

3e4r


Resolution: 1.7→26.14 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.722 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21303 1128 5 %RANDOM
Rwork0.1631 ---
obs0.16579 22426 83.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.543 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.01 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→26.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 28 210 2426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222271
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0341.9863100
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1175290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76322.67486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26315354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0341519
X-RAY DIFFRACTIONr_chiral_restr0.1350.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211702
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2431.51445
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.01722307
X-RAY DIFFRACTIONr_scbond_it3.6723826
X-RAY DIFFRACTIONr_scangle_it5.854.5792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 34 -
Rwork0.288 701 -
obs--36.99 %

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