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- PDB-9fct: BtuJ1 - Bacteroides thetaiotaomicron B12 scavenging protein -

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Basic information

Entry
Database: PDB / ID: 9fct
TitleBtuJ1 - Bacteroides thetaiotaomicron B12 scavenging 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: 1.603 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: To Be Published
Title: To be released (2024).
Authors: Juodeikis, R. / Ulrich, R. / Clarke, C. / Banasik, M. / Warren, M. / Pickersgill, R.
History
DepositionMay 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)60,4134
Polymers57,7002
Non-polymers2,7132
Water8,953497
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-19 kcal/mol
Surface area21670 Å2
Unit cell
Length a, b, c (Å)148.891, 51.416, 108.757
Angle α, β, γ (deg.)90, 131.789, 90
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: B / Label asym-ID: A / Auth seq-ID: 27 - 255 / Label seq-ID: 27 - 255

Dom-ID
1
2

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

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Components

#1: Protein DUF4465 domain-containing protein


Mass: 28850.016 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_1491 / Plasmid: pET14b / Details (production host): Ampicillin resistance / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q8A7N3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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
REFMAC5.8.0425refinement
autoPROC1.1.7data reduction
STARANISO2.3.94data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.603→81.09 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.198 / SU B: 4.605 / SU ML: 0.077 / Average fsc free: 0.9646 / Average fsc work: 0.971 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.098
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2132 3429 5.175 %
Rwork0.1886 62828 -
all0.19 --
obs-66257 82.048 %
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: 20.543 Å2
Baniso -1Baniso -2Baniso -3
1-0.128 Å2-0 Å20.159 Å2
2---1.048 Å2-0 Å2
3---0.245 Å2
Refinement stepCycle: LAST / Resolution: 1.603→81.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3674 0 186 497 4357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0123970
X-RAY DIFFRACTIONr_bond_other_d0.0070.0153510
X-RAY DIFFRACTIONr_angle_refined_deg2.3511.8745437
X-RAY DIFFRACTIONr_angle_other_deg1.4011.8318104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6475459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.45952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.09610627
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.03910189
X-RAY DIFFRACTIONr_chiral_restr0.1110.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024667
X-RAY DIFFRACTIONr_gen_planes_other0.010.02957
X-RAY DIFFRACTIONr_nbd_refined0.1420.2532
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1150.23004
X-RAY DIFFRACTIONr_nbtor_refined0.1490.21868
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0590.21909
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.080.2336
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0830.231
X-RAY DIFFRACTIONr_nbd_other0.1110.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.10.256
X-RAY DIFFRACTIONr_mcbond_it1.1720.9341842
X-RAY DIFFRACTIONr_mcbond_other1.1720.9341842
X-RAY DIFFRACTIONr_mcangle_it2.0441.6792299
X-RAY DIFFRACTIONr_mcangle_other2.0441.682300
X-RAY DIFFRACTIONr_scbond_it1.3881.0612128
X-RAY DIFFRACTIONr_scbond_other1.3881.062129
X-RAY DIFFRACTIONr_scangle_it2.2951.8563138
X-RAY DIFFRACTIONr_scangle_other2.2941.8563139
X-RAY DIFFRACTIONr_lrange_it7.50313.0974409
X-RAY DIFFRACTIONr_lrange_other6.59310.5724274
X-RAY DIFFRACTIONr_ncsr_local_group_10.0660.057463
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.065650.05009
12BX-RAY DIFFRACTIONLocal ncs0.065650.05009
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
1.603-1.6450.245240.2744890.27359100.9530.9468.68020.27
1.645-1.690.296910.27614680.27757590.9340.94427.07070.269
1.69-1.7390.2611630.27833070.27756430.9530.94561.49210.271
1.739-1.7920.2812280.2642390.26154530.9440.95281.91820.248
1.792-1.8510.272760.25145380.25253270.9480.95790.36980.236
1.851-1.9160.2482560.23546130.23551360.9570.96394.80140.218
1.916-1.9880.2372460.21945320.2249450.9620.96796.62280.203
1.988-2.0690.2272550.20144700.20247960.970.97598.51960.189
2.069-2.1610.2272260.19542660.19645270.9670.97399.22690.187
2.161-2.2660.2072310.18241640.18344180.9750.97999.47940.176
2.266-2.3890.2342200.17539150.17841510.9640.9899.61450.172
2.389-2.5340.2211930.17437550.17639620.970.98199.64660.175
2.534-2.7080.2471820.18930040.19237280.9670.97985.46140.194
2.708-2.9250.2321370.18233160.18434720.9670.97999.45280.197
2.925-3.2040.2041550.17329910.17531740.9740.98199.11780.193
3.204-3.5810.1791420.16527430.16629040.9840.98399.34570.189
3.581-4.1340.1711420.15924290.15925760.9820.98599.80590.183
4.134-5.060.1581220.14520530.14621790.9860.98899.81640.179
5.06-7.1420.182870.17716250.17817170.9840.98299.70880.225
7.142-81.090.201530.2039110.2029780.9680.97198.56850.277
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7138-0.12070.18821.4158-0.08221.55450.0392-0.0587-0.08240.0031-0.0486-0.01090.0810.04690.00950.03490.00590.01020.05530.01560.01053.5567-14.017927.3716
21.3208-0.06350.14231.3964-0.14931.52030.0063-0.0070.0479-0.0054-0.018-0.0095-0.02130.0290.01170.0049-0.00790.0090.057-0.00820.019923.9554-0.8241.5441
Refinement TLS groupSelection: ALL

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