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

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Basic information

Entry
Database: PDB / ID: 8baw
TitleX-ray structure of the CeuE Homologue from Geobacillus stearothermophilus - 5-LICAM siderophore analogue complex.
ComponentsSiderophore ABC transporter substrate-binding protein
KeywordsMETAL TRANSPORT / Periplasmic / Siderophore binding protein / Bacterial / siderophore analogue complex. / 5-LICAM
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 / N,N'-pentane-1,5-diylbis(2,3-dihydroxybenzamide) / : / Siderophore ABC transporter substrate-binding protein
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.471 Å
AuthorsBlagova, E.V. / Miller, A. / 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
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

Downloads & links

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Assembly

Deposited unit
A: Siderophore ABC transporter substrate-binding protein
B: Siderophore ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6326
Polymers66,7722
Non-polymers8604
Water3,639202
1
A: Siderophore ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8163
Polymers33,3861
Non-polymers4302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Siderophore ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8163
Polymers33,3861
Non-polymers4302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.395, 34.432, 119.109
Angle α, β, γ (deg.)90.000, 92.889, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Siderophore ABC transporter substrate-binding protein


Mass: 33385.930 Da / Num. of mol.: 2
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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C19H22N2O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus A12: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.03M of each divalent cation (MgCl2, CaCl2), 0.1M Bicine/Trizma base pH 8.5 5mM Fe(III) 5-LICAM 1:10 ratio protein:ligand. No cryo.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.93622 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Oct 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93622 Å / Relative weight: 1
ReflectionResolution: 1.47→67.4 Å / Num. obs: 93663 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.026 / Rrim(I) all: 0.048 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.05-67.315.20.025450.9990.0130.023
1.47-1.56.32.8646200.4321.863.423

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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: 8PBX

8pbx


Resolution: 1.471→67.4 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.177 / SU B: 6.303 / SU ML: 0.095 / Average fsc free: 0.9353 / Average fsc work: 0.9501 / 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
Rfree0.2326 4698 5.017 %
Rwork0.1797 88945 -
all0.182 --
obs-93643 99.791 %
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: 42.224 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å2-0 Å2-1.192 Å2
2---1.941 Å2-0 Å2
3---0.042 Å2
Refinement stepCycle: LAST / Resolution: 1.471→67.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4357 0 56 202 4615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124527
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164282
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.6546098
X-RAY DIFFRACTIONr_angle_other_deg0.4641.57210021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3265555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.784510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30210844
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.28110191
X-RAY DIFFRACTIONr_chiral_restr0.0670.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024969
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02803
X-RAY DIFFRACTIONr_nbd_refined0.2250.2814
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.23936
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22187
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22417
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2172
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0530.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.26
X-RAY DIFFRACTIONr_nbd_other0.1810.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2150.29
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0510.21
X-RAY DIFFRACTIONr_mcbond_it7.8614.1612220
X-RAY DIFFRACTIONr_mcbond_other7.8524.1612220
X-RAY DIFFRACTIONr_mcangle_it8.0126.2212775
X-RAY DIFFRACTIONr_mcangle_other8.0126.2242776
X-RAY DIFFRACTIONr_scbond_it8.1274.6042307
X-RAY DIFFRACTIONr_scbond_other8.1254.6032308
X-RAY DIFFRACTIONr_scangle_it9.1366.693323
X-RAY DIFFRACTIONr_scangle_other9.1356.693324
X-RAY DIFFRACTIONr_lrange_it9.14150.9994933
X-RAY DIFFRACTIONr_lrange_other9.14250.7954909
X-RAY DIFFRACTIONr_rigid_bond_restr8.28138807
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
1.471-1.5090.3623310.3665590.3669240.8570.88399.5090.367
1.509-1.550.3333230.34563360.34466730.90.88299.79020.347
1.55-1.5950.313260.31261690.31264970.9020.90599.96920.312
1.595-1.6440.3142890.29761080.29863980.8990.91299.98440.291
1.644-1.6980.33290.26257730.26461020.9280.9391000.252
1.698-1.7580.313140.2556320.25359500.920.94799.93280.232
1.758-1.8240.2882570.2255020.22357590.9350.9631000.199
1.824-1.8980.2552790.18552330.18955280.9540.97399.71060.162
1.898-1.9830.2582800.17850180.18252990.9530.97699.98110.155
1.983-2.0790.2432290.16748300.1750600.9610.97899.98020.148
2.079-2.1920.2492640.17246020.17748660.9570.981000.155
2.192-2.3240.222210.16543970.16846180.9650.9821000.151
2.324-2.4850.2492380.16640630.1743030.9580.98299.95350.154
2.485-2.6830.2511880.16538520.16940400.9630.9831000.156
2.683-2.9390.2611770.18435370.18837140.960.9791000.181
2.939-3.2850.2611550.232140.20333690.9530.9741000.202
3.285-3.7920.2271680.17328380.17630060.9690.9841000.182
3.792-4.640.1961360.1423990.14325380.9750.98899.88180.157
4.64-6.5470.1751140.13918990.14120160.9830.9999.85120.158
6.547-67.40.172800.1669850.16611790.9840.98390.33080.19

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