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- PDB-9i2l: BtuJ2 - DUF4465 domain containing protein -

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Basic information

Entry
Database: PDB / ID: 9i2l
TitleBtuJ2 - DUF4465 domain containing protein
ComponentsDUF4465 domain-containing protein
KeywordsMEMBRANE PROTEIN / Outer membrane / B12 binding / Lipoprotein
Function / homologyProtein of unknown function DUF4465 / Domain of unknown function (DUF4465) / Prokaryotic membrane lipoprotein lipid attachment site profile. / CYANOCOBALAMIN / DUF4465 domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsClarke, C. / Banasik, M. / Pickersgill, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X001946/1 United Kingdom
CitationJournal: Biochem.J. / Year: 2025
Title: Extracellular Vesicle-Linked Vitamin B12 Acquisition via Novel Binding Proteins in Bacteroides thetaiotaomicron.
Authors: Juodeikis, R. / Ulrich, R. / Clarke, C. / Banasik, M. / Deery, E. / Saalbach, G. / Krautler, B. / Carding, S.R. / Geeves, M.A. / Pickersgill, R. / Warren, M.J.
History
DepositionJan 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: DUF4465 domain-containing protein
A: DUF4465 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4136
Polymers67,6202
Non-polymers2,7934
Water95553
1
B: DUF4465 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2073
Polymers33,8101
Non-polymers1,3962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DUF4465 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2073
Polymers33,8101
Non-polymers1,3962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.746, 97.98, 70.472
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 49 - 303 / Label seq-ID: 50 - 304

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein DUF4465 domain-containing protein


Mass: 33810.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Lipoprotein export sequence removed, His-tagged
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_1957 / Plasmid: pET14b / Details (production host): Ampicillin resistance / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q8A6C7
#2: Chemical ChemComp-CNC / CYANOCOBALAMIN


Mass: 1356.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H89CoN14O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.4 % / Description: Shards with a distinctly red color
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 29% w/v PEG, 0.2M sodium citrate pH 3.5 / PH range: 3-4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.6→81.09 Å / Num. obs: 66258 / % possible obs: 82 % / Redundancy: 4.4 % / Biso Wilson estimate: 13.12 Å2 / CC1/2: 0.968 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.1 / Rrim(I) all: 0.2 / Net I/σ(I): 1.7
Reflection shellResolution: 1.6→1.7 Å / Num. unique obs: 66258 / CC1/2: 0.381

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
autoPROC1.1.7data reduction
STARANISO2.3.94data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→70.472 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.856 / WRfactor Rfree: 0.228 / WRfactor Rwork: 0.161 / SU B: 16.605 / SU ML: 0.317 / Average fsc free: 0.9457 / Average fsc work: 0.9685 / Cross valid method: THROUGHOUT / ESU R Free: 0.392
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2609 754 4.823 %
Rwork0.1849 14881 -
all0.188 --
obs-15635 97.89 %
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: 38.391 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2--0.951 Å2-0 Å2
3----0.531 Å2
Refinement stepCycle: LAST / Resolution: 2.73→70.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4069 0 188 53 4310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124388
X-RAY DIFFRACTIONr_bond_other_d0.0030.0153786
X-RAY DIFFRACTIONr_angle_refined_deg2.5061.8466047
X-RAY DIFFRACTIONr_angle_other_deg1.0241.7798678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6335512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.282510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95210598
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.82910216
X-RAY DIFFRACTIONr_chiral_restr0.1160.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025317
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021127
X-RAY DIFFRACTIONr_nbd_refined0.2030.2827
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.23732
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22168
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22262
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2110
X-RAY DIFFRACTIONr_metal_ion_refined0.3150.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1680.215
X-RAY DIFFRACTIONr_nbd_other0.1730.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1080.26
X-RAY DIFFRACTIONr_mcbond_it4.7513.7092060
X-RAY DIFFRACTIONr_mcbond_other4.7513.712060
X-RAY DIFFRACTIONr_mcangle_it6.9176.6592568
X-RAY DIFFRACTIONr_mcangle_other6.9186.662569
X-RAY DIFFRACTIONr_scbond_it5.3113.9792328
X-RAY DIFFRACTIONr_scbond_other5.313.9782329
X-RAY DIFFRACTIONr_scangle_it7.8067.1613479
X-RAY DIFFRACTIONr_scangle_other7.8057.163480
X-RAY DIFFRACTIONr_lrange_it9.55537.1774875
X-RAY DIFFRACTIONr_lrange_other9.55537.1774875
X-RAY DIFFRACTIONr_ncsr_local_group_10.1060.058253
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.106220.05009
12AX-RAY DIFFRACTIONLocal ncs0.106220.05009
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
2.73-2.8010.374490.32710890.32911590.910.91398.18810.306
2.801-2.8770.372370.28710960.28911370.9110.9499.64820.266
2.877-2.9610.398460.26810310.27310770.9170.9481000.234
2.961-3.0520.305530.23610060.23910600.9360.95999.90570.205
3.052-3.1520.293500.2149810.21810310.9330.9671000.188
3.152-3.2620.285490.1979710.20110200.9440.9721000.168
3.262-3.3850.255600.1929060.1959660.9520.9751000.166
3.385-3.5230.237430.1857660.1889400.9620.97786.06380.157
3.523-3.6790.23480.1487320.1529070.9660.98685.99780.131
3.679-3.8580.185410.1478100.1498510.9850.9871000.13
3.858-4.0660.317410.1667380.1748290.8710.98193.96860.151
4.066-4.3120.192440.1757390.1767830.9750.9781000.158
4.312-4.6080.264300.1317030.1367350.9590.98899.72790.124
4.608-4.9760.203340.1356640.1396980.9760.9881000.125
4.976-5.4480.268270.1436200.1476470.9620.9881000.132
5.448-6.0860.205230.1655560.1675790.9730.9861000.154
6.086-7.0190.224260.1464890.1495150.9680.9881000.139
7.019-8.5750.299230.174290.1764520.9480.981000.165
8.575-12.0390.237170.1693440.1723610.9620.9821000.173
12.039-70.4720.289130.2662110.2682250.9640.95799.55560.268

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