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- PDB-8bj9: X-ray structure of the CeuE Homologue from Parageobacillus thermo... -

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Basic information

Entry
Database: PDB / ID: 8bj9
TitleX-ray structure of the CeuE Homologue from Parageobacillus thermoglucosidasius - 5LICAM 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. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N,N'-pentane-1,5-diylbis(2,3-dihydroxybenzamide) / : / NICKEL (II) ION / ABC transporter
Similarity search - Component
Biological speciesParageobacillus thermoglucosidasius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.069 Å
AuthorsBlagova, E.V. / Bennett, M. / Booth, R. / Dodson, E.J. / Duhme-KLair, A.-K. / Wilson, K.S.
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
DepositionNov 3, 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

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Assembly

Deposited unit
A: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4798
Polymers32,7181
Non-polymers7617
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-41 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.063, 117.392, 141.712
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

21A-307-

SO4

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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, 19 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-5LC / N,N'-pentane-1,5-diylbis(2,3-dihydroxybenzamide)


Mass: 374.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N2O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / 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.: 12 / 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: 46.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Opt 17. E9. 18% PEG 3350, 0.1M TRIS, pH8.5, 0.05M ZnAc, Cryo ethylene glycol. Ligand: 5mM Fe(III) 5-LICAM 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: 0.976238 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Oct 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976238 Å / Relative weight: 1
ReflectionResolution: 2.069→36.83 Å / Num. obs: 18904 / % possible obs: 99.7 % / Redundancy: 23.1 % / CC1/2: 0.988 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.029 / Rrim(I) all: 0.105 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.02-36.821.60.0522740.9980.0150.054
2.07-2.13133.36315260.2381.3963.648

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
REFMAC5.8.0352refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BF6

8bf6


Resolution: 2.069→36.827 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.27 / WRfactor Rwork: 0.223 / SU B: 20.317 / SU ML: 0.225 / Average fsc free: 0.919 / Average fsc work: 0.9343 / Cross valid method: FREE R-VALUE / ESU R: 0.219 / ESU R Free: 0.197
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2656 938 4.979 %
Rwork0.2097 17902 -
all0.213 --
obs-18840 99.493 %
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: 84.136 Å2
Baniso -1Baniso -2Baniso -3
1-3.691 Å2-0 Å20 Å2
2---4.534 Å2-0 Å2
3---0.843 Å2
Refinement stepCycle: LAST / Resolution: 2.069→36.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2167 0 37 12 2216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122245
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162135
X-RAY DIFFRACTIONr_angle_refined_deg1.251.6493015
X-RAY DIFFRACTIONr_angle_other_deg0.4191.5674993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0995277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.78956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.91210417
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.7071093
X-RAY DIFFRACTIONr_chiral_restr0.0590.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022465
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02395
X-RAY DIFFRACTIONr_nbd_refined0.2410.2469
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21998
X-RAY DIFFRACTIONr_nbtor_refined0.180.21103
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21231
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.271
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.5230.229
X-RAY DIFFRACTIONr_nbd_other0.1220.217
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.310.29
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0960.22
X-RAY DIFFRACTIONr_mcbond_it3.2855.2621111
X-RAY DIFFRACTIONr_mcbond_other3.2855.2621111
X-RAY DIFFRACTIONr_mcangle_it4.3617.8911387
X-RAY DIFFRACTIONr_mcangle_other4.3597.8911388
X-RAY DIFFRACTIONr_scbond_it3.6365.531134
X-RAY DIFFRACTIONr_scbond_other3.4565.5341126
X-RAY DIFFRACTIONr_scangle_it5.0968.1741628
X-RAY DIFFRACTIONr_scangle_other5.0348.1741623
X-RAY DIFFRACTIONr_lrange_it6.82565.3032510
X-RAY DIFFRACTIONr_lrange_other6.82565.2742510
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
2.069-2.1230.444560.42112860.42214050.7540.7995.5160.42
2.123-2.1810.403630.36312580.36513220.8750.87699.92440.368
2.181-2.2440.352790.3512190.3513050.8720.85499.46360.351
2.244-2.3120.375630.32111710.32412350.8820.90299.9190.317
2.312-2.3880.373570.27711830.28212460.9290.94399.51850.271
2.388-2.4710.337630.26511150.26811810.9450.94899.7460.246
2.471-2.5640.364590.2711140.27511740.9290.95699.91480.251
2.564-2.6680.282410.23810610.2411030.9550.96499.90930.215
2.668-2.7860.266650.24310000.24410670.9390.96899.81260.223
2.786-2.9210.29530.2429580.24510110.9540.9681000.225
2.921-3.0780.299530.2529250.2559790.9330.96499.89790.238
3.078-3.2640.291360.248910.2429280.9560.96499.89220.232
3.264-3.4870.35400.2388220.2438620.9050.9661000.238
3.487-3.7640.225380.2457750.2448130.9690.9671000.256
3.764-4.1190.198460.1877150.1887610.9710.9781000.203
4.119-4.5980.204350.156580.1536930.9750.9841000.171
4.598-5.2950.321330.1595800.1676130.9520.9821000.186
5.295-6.4520.309280.215020.2165300.9190.9721000.238
6.452-8.9870.184220.1594140.1614360.9760.9831000.187
8.987-36.8270.18480.162550.1612680.9850.98198.13430.209
Refinement TLS params.Method: refined / Origin x: 9.3597 Å / Origin y: 8.0893 Å / Origin z: -17.6544 Å
111213212223313233
T0.0845 Å2-0.0269 Å20.0092 Å2-0.2988 Å2-0.0639 Å2--0.1939 Å2
L2.2004 °20.4577 °20.505 °2-3.3853 °21.3109 °2--3.0798 °2
S-0.0586 Å °-0.3584 Å °0.6187 Å °0.1776 Å °-0.0048 Å °0.2415 Å °-0.3693 Å °0.1448 Å °0.0635 Å °
Refinement TLS groupSelection: ALL

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