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- PDB-3fxb: Crystal structure of the ectoine-binding protein UehA -

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Basic information

Entry
Database: PDB / ID: 3fxb
TitleCrystal structure of the ectoine-binding protein UehA
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsTRANSPORT PROTEIN / PERIPLASMIC SUBSTRATE BINDING PROTEIN / selectivity helix / transport / membrane
Function / homology
Function and homology information


C4-dicarboxylate transmembrane transporter activity / C4-dicarboxylate transport / periplasmic space
Similarity search - Function
Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4CS / Ectoine/5-hydroxyectoine-binding periplasmic protein UehA
Similarity search - Component
Biological speciesSilicibacter pomeroyi DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLecher, J. / Pittelkow, M. / Bursy, J. / Smits, S.H.J. / Schmitt, L. / Bremer, E.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The crystal structure of UehA in complex with ectoine-A comparison with other TRAP-T binding proteins.
Authors: Lecher, J. / Pittelkow, M. / Zobel, S. / Bursy, J. / Bonig, T. / Smits, S.H. / Schmitt, L. / Bremer, E.
History
DepositionJan 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: TRAP dicarboxylate transporter, DctP subunit
B: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2704
Polymers72,9852
Non-polymers2842
Water00
1
A: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6352
Polymers36,4931
Non-polymers1421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6352
Polymers36,4931
Non-polymers1421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.000, 61.300, 86.300
Angle α, β, γ (deg.)90.00, 102.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 1 / Auth seq-ID: 1 - 310 / Label seq-ID: 15 - 324

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA

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Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 36492.641 Da / Num. of mol.: 2 / Fragment: UNP residues 28-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi DSS-3 (bacteria) / Strain: DSS-3 / DSM 15171 / Gene: SPO1147 / Plasmid: pBJ20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5LUA7
#2: Chemical ChemComp-4CS / (4S)-2-METHYL-1,4,5,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID / ECTOINE


Mass: 142.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N2O2

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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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM Na Citrate pH 5.6-6.0, 2.4-2.6M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 14412 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 44.69 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 11.32
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2VPO

2vpo


Resolution: 2.9→19.86 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.874 / SU B: 44.893 / SU ML: 0.366 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26161 718 5 %RANDOM
Rwork0.218 ---
obs0.22009 13642 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.083 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.01 Å2
2--0.03 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4862 0 20 0 4882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224996
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9651.9576788
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.075618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.49826.179246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40115816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.631158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023850
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.180.22135
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.23486
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0450.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2661.53184
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.38725000
X-RAY DIFFRACTIONr_scbond_it0.52232052
X-RAY DIFFRACTIONr_scangle_it0.8474.51788
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 2433 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.010.05
tight thermal0.020.5
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 51 -
Rwork0.327 988 -
obs--100 %
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)
14.6998-0.0609-1.15363.5513-0.7882.91920.2325-0.25380.28120.20530.06020.2111-0.11650.0731-0.2927-0.08570.03830.0579-0.15890.0265-0.2114-7.265-8.81815.645
22.90980.2196-1.78243.1309-2.44047.3791-0.2481-0.4327-0.2419-0.18510.0153-0.5180.49350.84760.2328-0.0740.1557-0.00010.0493-0.0009-0.104911.893-18.1566.131
33.9934-1.0077-2.71924.4296-0.41776.6945-0.19880.3209-0.09970.1878-0.12180.23860.5736-0.54560.3206-0.1472-0.03310.0409-0.1184-0.0713-0.14826.1656.98249.627
46.0563-1.6648-3.12354.70380.3934.66840.2130.67330.1782-0.5985-0.093-0.1603-0.39-0.512-0.12-0.05720.0742-0.00010.08160.0671-0.144716.18116.86230.975
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 75
2X-RAY DIFFRACTION1A91 - 121
3X-RAY DIFFRACTION1A210 - 245
4X-RAY DIFFRACTION2A76 - 90
5X-RAY DIFFRACTION2A122 - 209
6X-RAY DIFFRACTION2A246 - 310
7X-RAY DIFFRACTION3B1 - 75
8X-RAY DIFFRACTION3B91 - 121
9X-RAY DIFFRACTION3B210 - 245
10X-RAY DIFFRACTION4B76 - 90
11X-RAY DIFFRACTION4B122 - 209
12X-RAY DIFFRACTION4B246 - 310

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