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- PDB-8b7x: X-ray structure of the CeuE Homologue from Geobacillus stearother... -

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Basic information

Entry
Database: PDB / ID: 8b7x
TitleX-ray structure of the CeuE Homologue from Geobacillus stearothermophilus - apo form.
ComponentsSiderophore ABC transporter substrate-binding protein
KeywordsMETAL TRANSPORT / Periplasmic / Siderophore binding / Bacterial / apo protein.
Function / homologyFatB domain / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile. / iron ion transport / Chem-JEF / Siderophore ABC transporter substrate-binding protein
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsWilson, K.S. / Duhme-Klair, A.K. / Blagova, E.V. / Bennett, M.
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 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 / pdbx_validate_planes
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site / _pdbx_validate_planes.type
Revision 1.3Sep 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Feb 7, 2024Group: Refinement description / Category: 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)34,0803
Polymers33,3861
Non-polymers6942
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.519, 35.725, 52.290
Angle α, β, γ (deg.)81.566, 83.242, 65.060
Int Tables number1
Space group name H-MP1

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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-JEF / O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) / JEFFAMINE


Mass: 597.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H63NO10
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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 % sol: 26.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Index D3: 0.1M HEPES, pH 7.0, 30% Jeffamine ED 2001, pH 7.0. No cryo.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.42→32.225 Å / Num. obs: 37722 / % possible obs: 94.9 % / Redundancy: 2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.033 / Rrim(I) all: 0.046 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.78-32.22.10.0253890.9960.0250.035
1.42-1.441.70.32331720.8620.3230.457

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
REFMAC5.8.0352refinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zkw

3zkw


Resolution: 1.42→32.225 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.179 / SU B: 6.73 / SU ML: 0.105 / Average fsc free: 0.9556 / Average fsc work: 0.9828 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.085
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2281 1940 5.152 %
Rwork0.1655 35717 -
all0.169 --
obs-37657 94.67 %
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: 28.729 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.076 Å21.675 Å2
2---0.664 Å2-1.253 Å2
3---0.549 Å2
Refinement stepCycle: LAST / Resolution: 1.42→32.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 24 56 2254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122249
X-RAY DIFFRACTIONr_bond_other_d0.0040.0162144
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.6513031
X-RAY DIFFRACTIONr_angle_other_deg0.481.5715019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.76853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88710420
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.7371096
X-RAY DIFFRACTIONr_chiral_restr0.0690.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022453
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02395
X-RAY DIFFRACTIONr_nbd_refined0.2210.2412
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21973
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21094
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21199
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.262
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.232
X-RAY DIFFRACTIONr_nbd_other0.1820.2123
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2210.212
X-RAY DIFFRACTIONr_mcbond_it4.4152.6671109
X-RAY DIFFRACTIONr_mcbond_other4.4172.671110
X-RAY DIFFRACTIONr_mcangle_it5.434.0051385
X-RAY DIFFRACTIONr_mcangle_other5.4284.0091386
X-RAY DIFFRACTIONr_scbond_it6.2273.1991140
X-RAY DIFFRACTIONr_scbond_other5.8133.1731137
X-RAY DIFFRACTIONr_scangle_it6.8714.5811646
X-RAY DIFFRACTIONr_scangle_other6.4695.4481641
X-RAY DIFFRACTIONr_lrange_it7.15249.7442462
X-RAY DIFFRACTIONr_lrange_other7.15649.9022454
X-RAY DIFFRACTIONr_rigid_bond_restr6.21234390
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
1.42-1.4570.3611250.28124420.28528970.9090.96688.60890.296
1.457-1.4970.3451460.26225030.26628940.930.96991.53420.275
1.497-1.540.2881170.23524860.23827890.9570.97993.33090.245
1.54-1.5870.2891480.20323610.20826900.9610.98493.27140.212
1.587-1.6390.2721330.20823400.21126350.9640.98493.8520.212
1.639-1.6960.2851140.1922660.19525490.9530.98693.36990.192
1.696-1.760.2861070.20922040.21324170.940.9895.61440.212
1.76-1.8320.2871220.1921010.19523680.9530.98593.87670.188
1.832-1.9130.2871390.17220300.17922740.9520.98695.38260.171
1.913-2.0060.2421000.15819490.16221530.9580.98995.16950.158
2.006-2.1140.202820.14718710.14920380.980.98995.82920.147
2.114-2.2420.2411200.16417600.16919650.960.98795.67430.167
2.242-2.3960.237970.15816810.16218230.9630.98897.53150.162
2.396-2.5870.246700.15815730.16216910.9690.98697.16140.166
2.587-2.8320.232760.17514700.17815710.9670.98398.40870.187
2.832-3.1630.205720.15913050.16214020.9710.98698.21680.174
3.163-3.6460.209550.15411860.15712740.9750.98797.40970.171
3.646-4.4520.152510.1299780.1310470.9870.99198.28080.151
4.452-6.2360.199430.157640.1538160.980.98998.89710.18
6.236-32.2250.181230.1464470.1484720.9750.98599.57630.175

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