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- PDB-8bax: X-ray structure of the CeuE Homologue from Geobacillus stearother... -

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Basic information

Entry
Database: PDB / ID: 8bax
TitleX-ray structure of the CeuE Homologue from Geobacillus stearothermophilus - azotochelin complex.
ComponentsSiderophore ABC transporter substrate-binding protein
KeywordsMETAL TRANSPORT / Periplasmic binding protein / Siderophore binding / Bacterial
Function / homologyFatB domain / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / iron ion transport / Prokaryotic membrane lipoprotein lipid attachment site profile. / Azotochelin / : / Siderophore ABC transporter substrate-binding protein
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsBlagova, E.V. / Miller, A. / Dodson, E.J. / Booth, R. / 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
DepositionOct 12, 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: Siderophore ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8603
Polymers33,3861
Non-polymers4742
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.158, 66.652, 117.055
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Siderophore ABC transporter substrate-binding protein


Mass: 33385.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: EPB69_07310 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A857MR34
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
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 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morph C8: 12.5% PEG1K; 12.5% PEG 3350; 12.5% MPD; 0.03M each NPS (NaNO3, Na2HPO4, (NH4)2SO4); 0.1M MOPS/HEPES pH7.5. Ligand: 1.67mM Fe azotochelin-sulf/pyr-Ir catalyst, 1:1 protein:ligand ratio.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.38→58.596 Å / Num. obs: 54541 / % possible obs: 97.5 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.051 / Rrim(I) all: 0.138 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.56-58.59611.70.1014230.9960.0390.108
1.38-1.414.24.43925980.4731.7524.775

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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: 8BPX

8bpx


Resolution: 1.38→58.596 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 10.099 / SU ML: 0.143 / Cross valid method: FREE R-VALUE / ESU R: 0.084 / ESU R Free: 0.079
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2622 2753 5.055 %
Rwork0.2141 51708 -
all0.217 --
obs-54461 97.353 %
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: 30.655 Å2
Baniso -1Baniso -2Baniso -3
1--3.51 Å20 Å2-0 Å2
2---4.427 Å20 Å2
3---7.937 Å2
Refinement stepCycle: LAST / Resolution: 1.38→58.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 31 95 2340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122305
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162168
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.6543107
X-RAY DIFFRACTIONr_angle_other_deg0.5131.5725076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.545282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.34556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99210428
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.6011099
X-RAY DIFFRACTIONr_chiral_restr0.070.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022543
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02410
X-RAY DIFFRACTIONr_nbd_refined0.2310.2438
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.22001
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21125
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21148
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.298
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1320.28
X-RAY DIFFRACTIONr_nbd_other0.2220.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2150.28
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0830.21
X-RAY DIFFRACTIONr_mcbond_it5.8262.8841131
X-RAY DIFFRACTIONr_mcbond_other5.8052.8811128
X-RAY DIFFRACTIONr_mcangle_it6.8344.3591412
X-RAY DIFFRACTIONr_mcangle_other6.8374.361411
X-RAY DIFFRACTIONr_scbond_it6.8283.411174
X-RAY DIFFRACTIONr_scbond_other6.8313.4121172
X-RAY DIFFRACTIONr_scangle_it7.3014.8781695
X-RAY DIFFRACTIONr_scangle_other7.2994.8781696
X-RAY DIFFRACTIONr_lrange_it7.38639.6462565
X-RAY DIFFRACTIONr_lrange_other7.39139.592555
X-RAY DIFFRACTIONr_rigid_bond_restr22.58234473
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
1.38-1.4160.4481870.49337030.49140760.8690.88795.43670.496
1.416-1.4550.4811860.45335930.45439510.7920.89995.64670.455
1.455-1.4970.4821930.40935550.41239000.8130.90296.10260.41
1.497-1.5430.4331680.3934230.39237570.8290.89495.58160.387
1.543-1.5930.41790.34933390.35136230.8950.92197.10190.343
1.593-1.6490.3621860.31332240.31635210.9330.93596.84750.305
1.649-1.7120.3091790.30531310.30534500.9410.94895.9420.292
1.712-1.7810.3281440.25430650.25732760.9260.97297.95480.239
1.781-1.8610.3091590.24929390.25231500.9560.97298.34920.233
1.861-1.9510.2551290.20528220.20730280.9740.98897.45710.19
1.951-2.0570.2791390.1926610.19428670.9540.98797.66310.178
2.057-2.1810.2411420.19225650.19527600.9650.98698.07970.183
2.181-2.3320.2561570.18523710.18925690.960.98498.40410.177
2.332-2.5180.241310.19222520.19524130.9580.9898.75670.187
2.518-2.7580.2681010.17921090.18222300.9630.98399.10310.18
2.758-3.0830.2541080.19119250.19420490.9590.97999.21910.201
3.083-3.5580.207840.17517050.17718040.9760.98299.16850.191
3.558-4.3530.215770.16114710.16315550.9720.98599.54980.188
4.353-6.140.217640.17411560.17612230.9760.98399.75470.212
6.14-58.5960.185400.1936990.1927400.9760.97499.86490.245

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