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- PDB-8bf6: X-ray structure of the CeuE Homologue from Parageobacillus thermo... -

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Basic information

Entry
Database: PDB / ID: 8bf6
TitleX-ray structure of the CeuE Homologue from Parageobacillus thermoglucosidasius - azotochelin complex
ComponentsABC transporter
KeywordsMETAL TRANSPORT / Periplasmic / Siderophore binding / Bacterial / apo protein
Function / homology
Function and homology information


FatB domain / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Azotochelin / : / NICKEL (II) ION / ABC transporter
Similarity search - Component
Biological speciesParageobacillus thermoglucosidasius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.969 Å
AuthorsWilson, K.S. / Duhme-Klair, A.-K. / Blagova, E.V. / Miller, A. / Booth, R. / Dodson, E.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)EP/T007338/1 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Thermostable homologues of the periplasmic siderophore-binding protein CeuE from Geobacillus stearothermophilus and Parageobacillus thermoglucosidasius.
Authors: Blagova, E.V. / Miller, A.H. / Bennett, M. / Booth, R.L. / Dodson, E.J. / Duhme-Klair, A.K. / Wilson, K.S.
History
DepositionOct 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 9, 2023Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5829
Polymers32,7181
Non-polymers8648
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-43 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.295, 116.711, 141.471
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-303-

NI

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ABC transporter


Mass: 32718.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parageobacillus thermoglucosidasius (bacteria)
Gene: BAA00_15370 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Y3Q1V3

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Non-polymers , 5 types, 37 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-95B / Azotochelin


Mass: 418.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N2O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 25% PEG 1500; 0.1 M PCMB pH 4.0 (Na propionate: Na cacodylate: BisTris propane 2:1:2). LIgand: 5mM Fe(III) Azotochelin (Washed) 1:10 ratio protein:ligand.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979499 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Aug 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979499 Å / Relative weight: 1
ReflectionResolution: 1.969→70.836 Å / Num. obs: 21889 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Net I/σ(I): 16.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.02-70.7411.30.022309010.0090.024
1.97-2.0213.32.703202390.4081.12.922

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8PBX

8pbx


Resolution: 1.969→70.836 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 13.281 / SU ML: 0.162 / Cross valid method: FREE R-VALUE / ESU R: 0.178 / ESU R Free: 0.167
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2547 1084 4.96 %
Rwork0.2048 20769 -
all0.207 --
obs-21853 99.963 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 59.941 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0 Å2
2---0.871 Å20 Å2
3---0.841 Å2
Refinement stepCycle: LAST / Resolution: 1.969→70.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2167 0 41 29 2237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122258
X-RAY DIFFRACTIONr_bond_other_d0.0150.0162134
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.6493022
X-RAY DIFFRACTIONr_angle_other_deg0.551.5674991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0955277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.52856
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.93910417
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.5041093
X-RAY DIFFRACTIONr_chiral_restr0.0580.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022469
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02395
X-RAY DIFFRACTIONr_nbd_refined0.2310.2466
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.22025
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21105
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21281
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.257
X-RAY DIFFRACTIONr_metal_ion_refined00.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4290.223
X-RAY DIFFRACTIONr_nbd_other0.1810.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3320.215
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0630.23
X-RAY DIFFRACTIONr_mcbond_it2.5384.1111114
X-RAY DIFFRACTIONr_mcbond_other2.5384.111111
X-RAY DIFFRACTIONr_mcangle_it3.3156.1561389
X-RAY DIFFRACTIONr_mcangle_other3.3146.1551388
X-RAY DIFFRACTIONr_scbond_it3.5114.4641144
X-RAY DIFFRACTIONr_scbond_other3.5064.4641132
X-RAY DIFFRACTIONr_scangle_it4.9766.5431633
X-RAY DIFFRACTIONr_scangle_other4.9796.541628
X-RAY DIFFRACTIONr_lrange_it6.14651.3232516
X-RAY DIFFRACTIONr_lrange_other6.1451.2752511
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.969-2.020.386830.35315110.35516010.8620.87699.56280.355
2.02-2.0750.366700.31714580.3215280.8920.9191000.317
2.075-2.1350.289660.2914540.2915200.9450.9381000.285
2.135-2.2010.294690.26313770.26514460.9480.9521000.255
2.201-2.2730.302830.24613590.24914420.9320.961000.233
2.273-2.3530.303700.22813090.23113790.9510.9691000.209
2.353-2.4420.249640.21112690.21313330.9570.9751000.191
2.442-2.5410.295640.21312080.21712730.9450.97499.92140.191
2.541-2.6540.227510.22411870.22412380.9680.971000.201
2.654-2.7830.296670.2211290.22511960.9450.9711000.2
2.783-2.9340.29640.22710360.23111000.9520.9681000.204
2.934-3.1110.302530.24310190.24610720.950.9631000.226
3.111-3.3260.259400.2379790.23810190.9650.9631000.225
3.326-3.5920.3440.2429050.2459490.9420.9671000.233
3.592-3.9330.246500.2248080.2258580.9750.9741000.216
3.933-4.3960.158450.1647530.1647980.9850.9851000.161
4.396-5.0730.27380.1436830.157210.9740.9881000.141
5.073-6.2050.294280.1715770.1776050.9690.9831000.168
6.205-8.7410.188270.1594580.164850.9810.9851000.155
8.741-70.8360.14680.1662900.1662980.9820.9751000.171
Refinement TLS params.Method: refined / Origin x: 9.6728 Å / Origin y: -8.0535 Å / Origin z: 17.6784 Å
111213212223313233
T0.044 Å20.0312 Å2-0.0026 Å2-0.087 Å2-0.0571 Å2--0.0665 Å2
L1.5474 °20.0056 °2-0.2171 °2-3.5639 °21.0343 °2--2.1693 °2
S-0.0182 Å °0.2833 Å °-0.3026 Å °-0.1941 Å °-0.0142 Å °0.1219 Å °0.1347 Å °0.1769 Å °0.0324 Å °
Refinement TLS groupSelection: ALL

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