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- PDB-2x26: Crystal structure of the periplasmic aliphatic sulphonate binding... -

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Basic information

Entry
Database: PDB / ID: 2x26
TitleCrystal structure of the periplasmic aliphatic sulphonate binding protein SsuA from Escherichia coli
ComponentsPERIPLASMIC ALIPHATIC SULPHONATES-BINDING PROTEIN
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


ABC-type alkanesulfonate transporter transporter activity / alkanesulfonate transmembrane transport / cellular response to sulfur starvation / sulfur compound metabolic process / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / Helix non-globular / Periplasmic binding protein-like II / 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 / Helix non-globular / Periplasmic binding protein-like II / Special / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative aliphatic sulfonates-binding protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBeale, J. / Lee, S. / Iwata, S. / Beis, K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of the Aliphatic Sulfonate-Binding Protein Ssua from Escherichia Coli
Authors: Beale, J. / Lee, S.Y. / Iwata, S. / Beis, K.
History
DepositionJan 11, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PERIPLASMIC ALIPHATIC SULPHONATES-BINDING PROTEIN
B: PERIPLASMIC ALIPHATIC SULPHONATES-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6454
Polymers67,4612
Non-polymers1842
Water7,674426
1
A: PERIPLASMIC ALIPHATIC SULPHONATES-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8232
Polymers33,7301
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PERIPLASMIC ALIPHATIC SULPHONATES-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8232
Polymers33,7301
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.891, 96.026, 142.401
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PERIPLASMIC ALIPHATIC SULPHONATES-BINDING PROTEIN


Mass: 33730.414 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-319
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL EXTENSION AFTER THE MATURE PROTEIN / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: GFPD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P75853
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.18 Å3/Da / Density % sol: 43.72 % / Description: NONE
Crystal growTemperature: 293 K / pH: 7.5
Details: 22% PEG3350, 0.2M SODIUM FORMATE AT 293K IN 2 DAYS, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 16, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.75→71.2 Å / Num. obs: 57014 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.7
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.8 / % possible all: 99.2

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
BALBESphasing
MOLREPphasing
REFMAC5.5.0106refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3E4R

3e4r


Resolution: 1.75→79.62 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.671 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. RESIDUES 320 TO 332 BELONG TO THE C-TERMINAL EXTENSION FROM THE CLONING VECTOR. THERE IS STILL SOME POSITIVE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. RESIDUES 320 TO 332 BELONG TO THE C-TERMINAL EXTENSION FROM THE CLONING VECTOR. THERE IS STILL SOME POSITIVE DENSITY OBSERVED AROUND RESIDUES B328-332. THIS IS BECAUSE WE HAVE MODELLED AND REFINED WITH 0.5 OCCUPANCY DUE TO CONFORMATION CHANGES.
RfactorNum. reflection% reflectionSelection details
Rfree0.22538 2889 5.1 %RANDOM
Rwork0.18585 ---
obs0.18784 54060 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.746 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å2-0 Å2
2--0.02 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.75→79.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4628 0 12 426 5066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224985
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9726821
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5135662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92324.672229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12915850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.511531
X-RAY DIFFRACTIONr_chiral_restr0.1090.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213853
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_it0.9091.53100
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55525020
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.61331885
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2484.51768
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 201 -
Rwork0.287 3953 -
obs--98.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.99860.1338-0.51560.9434-0.46521.38180.1204-0.12570.18930.0484-0.05170.0164-0.04130.1602-0.06860.0475-0.00270.02060.0961-0.01970.103930.445101.5966.05
20.81990.3849-0.88342.36910.34571.9128-0.08590.00240.0361-0.1766-0.05740.04350.5513-0.04360.14330.35530.00460.020.0836-0.00890.074420.66579.0997.169
31.62480.2505-0.18710.8293-0.71032.1248-0.06860.0524-0.2437-0.0684-0.0233-0.1030.12580.17220.09190.06040.00270.02280.08580.00090.075910.76698.683-28.124
42.4279-0.16590.43932.546-1.10354.1331-0.2473-0.03980.1850.1580.1075-0.0434-0.96540.13590.13980.3512-0.0531-0.04750.0420.00990.00490.948120.029-35.142
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 106
2X-RAY DIFFRACTION1A210 - 310
3X-RAY DIFFRACTION2A107 - 209
4X-RAY DIFFRACTION3B25 - 106
5X-RAY DIFFRACTION3B210 - 310
6X-RAY DIFFRACTION4B107 - 209

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