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- PDB-2q89: Crystal structure of EhuB in complex with hydroxyectoine -

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Basic information

Entry
Database: PDB / ID: 2q89
TitleCrystal structure of EhuB in complex with hydroxyectoine
ComponentsPutative ABC transporter amino acid-binding protein
KeywordsTRANSPORT PROTEIN / Compatible solutes / substrate-binding proteins / ABC-transporters / osmoprotection
Function / homology
Function and homology information


ectoine binding / ectoine transmembrane transport
Similarity search - Function
Ectoine/Hydroxyectoine ABC transporter, substrate-binding protein EhuB / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6CS / : / Cystine-binding periplasmic protein
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHanekop, N. / Hoeing, M. / Sohn-Bosser, L. / Jebbar, M. / Schmitt, L. / Bremer, E.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure of the ligand-binding protein EhuB from Sinorhizobium meliloti reveals substrate recognition of the compatible solutes ectoine and hydroxyectoine.
Authors: Hanekop, N. / Hoing, M. / Sohn-Bosser, L. / Jebbar, M. / Schmitt, L. / Bremer, E.
History
DepositionJun 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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: Putative ABC transporter amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7736
Polymers27,1651
Non-polymers6085
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.135, 57.135, 161.576
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Putative ABC transporter amino acid-binding protein / EhuB


Mass: 27164.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q92WC8
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-6CS / (4S,5S)-5-HYDROXY-2-METHYL-1,4,5,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID


Mass: 158.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 4
Details: sodium acetate PEG Cadmium chloride, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 12062 / % possible obs: 95.5 % / Rmerge(I) obs: 0.055 / Χ2: 0.908 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.340.2025670.78196.3
2.34-2.380.2146200.801196.6
2.38-2.430.1925730.846196.8
2.43-2.480.1866110.533196.5
2.48-2.530.1715650.936196.3
2.53-2.590.1446070.826196.7
2.59-2.650.1315840.89196.7
2.65-2.730.1326070.923196.2
2.73-2.810.1035930.953196.6
2.81-2.90.0936150.987197.2
2.9-30.0796001.011197.2
3-3.120.0736041.209197.1
3.12-3.260.0645981.199196.8
3.26-3.430.0556191.235197.2
3.43-3.650.0476080.939197
3.65-3.930.0436260.733196.5
3.93-4.320.0386140.723196.2
4.32-4.930.0356350.914196.5
4.93-6.180.0366410.893194.4
6.18-200.0355750.847178.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.896 / SU B: 13.556 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.416 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 589 4.9 %RANDOM
Rwork0.235 ---
obs0.236 12046 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.252 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å20 Å2
2--1.49 Å20 Å2
3----2.98 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 15 57 1978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221950
X-RAY DIFFRACTIONr_angle_refined_deg1.041.9862637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5235256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81224.93779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65815330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5231512
X-RAY DIFFRACTIONr_chiral_restr0.0630.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021483
X-RAY DIFFRACTIONr_nbd_refined0.1780.2917
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21328
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.290
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.211
X-RAY DIFFRACTIONr_mcbond_it0.3381.51322
X-RAY DIFFRACTIONr_mcangle_it0.58222041
X-RAY DIFFRACTIONr_scbond_it0.813697
X-RAY DIFFRACTIONr_scangle_it1.4194.5596
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 43 -
Rwork0.241 809 -
obs-852 96.49 %
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)
10.5860.44610.01211.5266-0.16961.63270.03370.07670.03580.0487-0.0034-0.0186-0.1142-0.0031-0.0303-0.09250.02790.0025-0.0021-0.0047-0.023624.273828.653122.942
22.08030.6246-1.29021.8723-0.35931.75490.0095-0.0614-0.07310.09690.0237-0.074-0.0251-0.002-0.0332-0.0512-0.0206-0.0081-0.03210.0056-0.046813.868113.345141.1483
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 981 - 99
2X-RAY DIFFRACTION1AA200 - 256201 - 257
3X-RAY DIFFRACTION2AA99 - 199100 - 200

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