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

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Basic information

Entry
Database: PDB / ID: 8bnw
TitleX-ray structure of the CeuE Homologue from Parageobacillus thermoglucosidasius - apo form
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
NICKEL (II) ION / ABC transporter
Similarity search - Component
Biological speciesParageobacillus thermoglucosidasius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.133 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 14, 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)33,2048
Polymers32,7181
Non-polymers4867
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-62 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.369, 118.433, 141.046
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#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
#2: Chemical
ChemComp-NI / NICKEL (II) ION


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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 Matthews: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 17% PEG 3350; 0.1M MES, pH 6.5, 0.1M MgAc; Cryo- EthGl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.13→70.623 Å / Num. obs: 17078 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Net I/σ(I): 17.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.05-70.5210.40.01826610.0070.019
2.13-2.1912.93.27213770.3771.3523.543

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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: 2.133→70.623 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 10.914 / SU ML: 0.252 / Cross valid method: FREE R-VALUE / ESU R: 0.261 / ESU R Free: 0.213
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2661 862 5.057 %
Rwork0.2216 16183 -
all0.224 --
obs-17045 99.93 %
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: 76.498 Å2
Baniso -1Baniso -2Baniso -3
1-1.572 Å2-0 Å20 Å2
2--0.088 Å2-0 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.133→70.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2167 0 15 9 2191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122224
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162112
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.6432984
X-RAY DIFFRACTIONr_angle_other_deg0.3881.5664944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.15277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.30554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98510417
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.5851093
X-RAY DIFFRACTIONr_chiral_restr0.0520.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022433
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02387
X-RAY DIFFRACTIONr_nbd_refined0.2340.2473
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.22057
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21079
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21235
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.070.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4470.237
X-RAY DIFFRACTIONr_nbd_other0.2240.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.290.210
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.3240.23
X-RAY DIFFRACTIONr_mcbond_it4.9627.661111
X-RAY DIFFRACTIONr_mcbond_other4.967.6591111
X-RAY DIFFRACTIONr_mcangle_it6.95411.4891387
X-RAY DIFFRACTIONr_mcangle_other6.95211.4921388
X-RAY DIFFRACTIONr_scbond_it5.6817.9481113
X-RAY DIFFRACTIONr_scbond_other5.4147.9581100
X-RAY DIFFRACTIONr_scangle_it8.10311.7791597
X-RAY DIFFRACTIONr_scangle_other7.82511.7841586
X-RAY DIFFRACTIONr_lrange_it10.572105.7192471
X-RAY DIFFRACTIONr_lrange_other10.572105.7392471
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
2.133-2.1880.397610.37911730.3812340.8820.8591000.382
2.188-2.2480.376740.36211160.36311900.8460.8771000.365
2.248-2.3130.39590.34811220.3511810.8940.8921000.349
2.313-2.3840.433530.31310950.31811480.8620.9231000.314
2.384-2.4620.324630.29410400.29511030.9150.9431000.288
2.462-2.5490.336540.32810240.32910790.920.93299.90730.317
2.549-2.6450.198340.3049970.310310.9740.9361000.285
2.645-2.7530.281580.2859460.28510040.9470.9451000.258
2.753-2.8750.376530.2499050.2569580.9420.9641000.223
2.875-3.0150.288530.2498680.2529210.9310.9661000.222
3.015-3.1780.301380.2538450.2558830.9490.9641000.225
3.178-3.370.275320.2667940.2668260.9510.9621000.25
3.37-3.6020.356350.2837700.2868050.9270.9521000.27
3.602-3.890.27480.2566740.2577220.9690.9641000.241
3.89-4.260.17380.1826530.1816910.980.9821000.174
4.26-4.760.202280.1435970.1456250.9720.9871000.135
4.76-5.4930.374290.1725160.1815450.9410.9821000.165
5.493-6.7170.213290.184590.1824880.9690.9791000.173
6.717-9.4560.231150.1593630.1623780.9730.9851000.145
9.456-70.6230.12680.1852260.1822400.9880.96697.50.154

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