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- PDB-4wep: Apo YehZ from Escerichia coli -

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Basic information

Entry
Database: PDB / ID: 4wep
TitleApo YehZ from Escerichia coli
ComponentsPutative osmoprotectant uptake system substrate-binding protein OsmF
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / osmoprotection / compatible solutes / glycine betaine
Function / homology
Function and homology information


amino-acid betaine transport / glycine betaine transport / cellular hyperosmotic response / amino acid transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / periplasmic space / membrane
Similarity search - Function
Osmoprotection protein (prox); domain 2 / ABC-type glycine betaine transport system, substrate-binding domain / Substrate binding domain of ABC-type glycine betaine transport system / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glycine betaine-binding protein YehZ
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKimber, M.S. / Lang, S. / Mendoza, K. / Wood, J.M.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)508-2008 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)327280 Canada
CitationJournal: Biochemistry / Year: 2015
Title: YehZYXW of Escherichia coli Is a Low-Affinity, Non-Osmoregulatory Betaine-Specific ABC Transporter.
Authors: Lang, S. / Cressatti, M. / Mendoza, K.E. / Coumoundouros, C.N. / Plater, S.M. / Culham, D.E. / Kimber, M.S. / Wood, J.M.
History
DepositionSep 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative osmoprotectant uptake system substrate-binding protein OsmF
B: Putative osmoprotectant uptake system substrate-binding protein OsmF


Theoretical massNumber of molelcules
Total (without water)64,3072
Polymers64,3072
Non-polymers00
Water12,088671
1
A: Putative osmoprotectant uptake system substrate-binding protein OsmF


Theoretical massNumber of molelcules
Total (without water)32,1531
Polymers32,1531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative osmoprotectant uptake system substrate-binding protein OsmF


Theoretical massNumber of molelcules
Total (without water)32,1531
Polymers32,1531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.740, 76.110, 91.490
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 Putative osmoprotectant uptake system substrate-binding protein OsmF


Mass: 32153.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: osmF, yehZ, b2131, JW2119 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 pREP4 / References: UniProt: P33362
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / 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: 1.94 Å3/Da / Density % sol: 36.67 % / Description: thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 25% (w/v) PEG 3350, 0.1 M citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 16, 2014
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 80739 / Num. obs: 80739 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rsym value: 0.082 / Net I/σ(I): 15.7
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 5 % / Rmerge(I) obs: 0.938 / Mean I/σ(I) obs: 1.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NE4

4ne4


Resolution: 1.5→45.745 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1926 4037 5 %random
Rwork0.1692 ---
obs0.1704 80736 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→45.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4268 0 0 671 4939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054434
X-RAY DIFFRACTIONf_angle_d0.9546050
X-RAY DIFFRACTIONf_dihedral_angle_d13.9271633
X-RAY DIFFRACTIONf_chiral_restr0.036690
X-RAY DIFFRACTIONf_plane_restr0.005792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51760.32081360.3312593X-RAY DIFFRACTION100
1.5176-1.53620.35561370.27932600X-RAY DIFFRACTION100
1.5362-1.55560.29691380.25582615X-RAY DIFFRACTION100
1.5556-1.57610.25371380.24142625X-RAY DIFFRACTION100
1.5761-1.59770.25341380.21472629X-RAY DIFFRACTION100
1.5977-1.62050.23241370.20522595X-RAY DIFFRACTION100
1.6205-1.64470.20971360.20142593X-RAY DIFFRACTION100
1.6447-1.67040.2021400.20122654X-RAY DIFFRACTION100
1.6704-1.69780.20991380.18612617X-RAY DIFFRACTION100
1.6978-1.7270.23921370.18342622X-RAY DIFFRACTION100
1.727-1.75840.1891400.17942641X-RAY DIFFRACTION100
1.7584-1.79230.21921360.17712592X-RAY DIFFRACTION100
1.7923-1.82890.21021390.17992640X-RAY DIFFRACTION100
1.8289-1.86860.20171370.17292614X-RAY DIFFRACTION100
1.8686-1.91210.1921390.17272636X-RAY DIFFRACTION100
1.9121-1.95990.19351380.17162614X-RAY DIFFRACTION100
1.9599-2.01290.19471390.16792649X-RAY DIFFRACTION100
2.0129-2.07210.19791390.16662631X-RAY DIFFRACTION100
2.0721-2.1390.20071390.16662642X-RAY DIFFRACTION100
2.139-2.21550.20231380.15662631X-RAY DIFFRACTION100
2.2155-2.30420.19721400.16552654X-RAY DIFFRACTION100
2.3042-2.4090.19431390.16592634X-RAY DIFFRACTION100
2.409-2.5360.19021410.16532687X-RAY DIFFRACTION100
2.536-2.69490.22631390.17392647X-RAY DIFFRACTION100
2.6949-2.90290.19771410.17532675X-RAY DIFFRACTION100
2.9029-3.1950.19291410.16672678X-RAY DIFFRACTION100
3.195-3.65720.18361430.15552712X-RAY DIFFRACTION100
3.6572-4.6070.11841430.13362719X-RAY DIFFRACTION100
4.607-45.76630.18911510.15882860X-RAY DIFFRACTION100
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)
11.36430.4135-0.37252.55360.81272.7821-0.05530.02470.0265-0.15270.00930.1320.0167-0.11320.03670.1218-0.00230.00010.09990.00640.101635.633834.09844.8783
20.9340.08190.39582.0980.39842.2735-0.0180.09120.0965-0.10720.0544-0.1407-0.00640.1835-0.02680.0865-0.00320.01430.13580.01640.151550.146554.662832.7321
32.74360.7463-0.99281.47960.59922.74770.00610.0348-0.1473-0.0071-0.0118-0.06430.0830.0389-0.00330.10230.0061-0.01490.0942-0.0090.1250.93217.21323.54
41.37470.36570.3421.3889-0.57182.45550.0122-0.12590.07040.1668-0.1232-0.0711-0.1768-0.02360.0940.13040.0063-0.01050.1253-0.00230.137470.808833.095735.1885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 129:240)
2X-RAY DIFFRACTION2chain 'A' and ((resseq 24:128) or (resseq 241:304))
3X-RAY DIFFRACTION3chain 'B' and (resseq 129:240)
4X-RAY DIFFRACTION4chain 'B' and ((resseq 24:128) or (resseq 241:304))

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