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- PDB-7biz: Structure of a B12 binding lipoprotein from Bacteroides thetaiota... -

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Basic information

Entry
Database: PDB / ID: 7biz
TitleStructure of a B12 binding lipoprotein from Bacteroides thetaiotaomicron
ComponentsCell surface protein
KeywordsUNKNOWN FUNCTION / B12 binding protein / lipoprotein
Function / homologyBacteroidetes PKD-like domain / PKD-like domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / CYANOCOBALAMIN / Cell surface protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsAbellon-Ruiz, J. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
CitationJournal: Mbio / Year: 2022
Title: Gut Commensal Bacteroidetes Encode a Novel Class of Vitamin B 12 -Binding Proteins.
Authors: Putnam, E.E. / Abellon-Ruiz, J. / Killinger, B.J. / Rosnow, J.J. / Wexler, A.G. / Folta-Stogniew, E. / Wright, A.T. / van den Berg, B. / Goodman, A.L.
History
DepositionJan 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4May 1, 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: Cell surface protein
B: Cell surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,01314
Polymers112,3092
Non-polymers7,70412
Water25,3111405
1
A: Cell surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6747
Polymers56,1551
Non-polymers4,5196
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3397
Polymers56,1551
Non-polymers3,1856
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.052, 128.052, 135.051
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cell surface protein / PKD domain protein / PKD-like domain protein


Mass: 56154.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BSIG_2898, Btheta7330_04243, DW011_18555, EH213_03063, F9Z91_12155, GAG59_23440, GAN91_25070, GAO00_20505, GAO05_10290, GAO06_11895, GAO10_09605, GAO29_13430, GAO30_12715, GAO37_11355, GAO39_ ...Gene: BSIG_2898, Btheta7330_04243, DW011_18555, EH213_03063, F9Z91_12155, GAG59_23440, GAN91_25070, GAO00_20505, GAO05_10290, GAO06_11895, GAO10_09605, GAO29_13430, GAO30_12715, GAO37_11355, GAO39_13880, GAO40_04505, GAO43_13395, GAO49_11265, GAO54_08270, GAO55_10400, GAO58_08100, GAO60_13260
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N7IAT3

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Non-polymers , 6 types, 1417 molecules

#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.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1405 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: Molecular dimensions. Morpheus condition B1 (0.1M Halogens (NaF, NaBr and NaI) 0.1M imidazole, 0.1 MES monohydrate acid pH6.5 and 30% precipitant mix 1 (40% v/v PEG500 MME, 20%W/V PEG 20000))

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96864 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96864 Å / Relative weight: 1
ReflectionResolution: 1.53→85.74 Å / Num. obs: 191916 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 20.85 Å2 / CC1/2: 0.99 / Net I/σ(I): 0.9
Reflection shellResolution: 1.53→1.58 Å / Num. unique obs: 19009 / CC1/2: 0.582

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Processing

Software
NameVersionClassification
DIALSdata processing
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIXv1.18_3855refinement
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-house structure

Resolution: 1.53→85.7 Å / SU ML: 0.1749 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 20.3513
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1916 9275 4.83 %
Rwork0.1649 355801 -
obs0.1662 191893 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.51 Å2
Refinement stepCycle: LAST / Resolution: 1.53→85.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7449 0 247 1405 9101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00897894
X-RAY DIFFRACTIONf_angle_d1.515810786
X-RAY DIFFRACTIONf_chiral_restr0.14781139
X-RAY DIFFRACTIONf_plane_restr0.00631373
X-RAY DIFFRACTIONf_dihedral_angle_d19.65172791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.550.3226400.298511761X-RAY DIFFRACTION99.15
1.55-1.570.29796180.283611853X-RAY DIFFRACTION99.88
1.57-1.580.28445410.27411836X-RAY DIFFRACTION99.85
1.58-1.60.29226400.266311936X-RAY DIFFRACTION99.9
1.6-1.630.28045920.258311776X-RAY DIFFRACTION99.94
1.63-1.650.27546080.258711879X-RAY DIFFRACTION99.97
1.65-1.670.2755700.250611854X-RAY DIFFRACTION99.94
1.67-1.70.27635850.24811922X-RAY DIFFRACTION99.97
1.7-1.720.26765860.236511851X-RAY DIFFRACTION99.97
1.72-1.750.22866360.218311763X-RAY DIFFRACTION99.96
1.75-1.780.24896580.202811891X-RAY DIFFRACTION99.98
1.78-1.810.21336060.194511833X-RAY DIFFRACTION99.96
1.81-1.850.19365660.183211901X-RAY DIFFRACTION99.99
1.85-1.890.19435280.170711902X-RAY DIFFRACTION100
1.89-1.930.19326720.166411838X-RAY DIFFRACTION99.93
1.93-1.970.17315480.162411919X-RAY DIFFRACTION99.96
1.97-2.020.19355180.162211931X-RAY DIFFRACTION100
2.02-2.080.19236300.161611876X-RAY DIFFRACTION100
2.08-2.140.18225780.157611858X-RAY DIFFRACTION99.98
2.14-2.210.18865940.155711857X-RAY DIFFRACTION99.99
2.21-2.290.17765880.152811933X-RAY DIFFRACTION99.98
2.29-2.380.1845620.160211889X-RAY DIFFRACTION100
2.38-2.480.20956640.158411791X-RAY DIFFRACTION99.99
2.48-2.620.19915940.163111873X-RAY DIFFRACTION100
2.62-2.780.19016280.16511874X-RAY DIFFRACTION100
2.78-2.990.20876060.164111830X-RAY DIFFRACTION99.99
2.99-3.30.17955860.160811884X-RAY DIFFRACTION100
3.3-3.770.17916450.143911827X-RAY DIFFRACTION100
3.77-4.750.15086670.127311799X-RAY DIFFRACTION100
4.75-85.70.16556050.14911864X-RAY DIFFRACTION99.94
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)
10.464094494253-0.0536362651404-0.2262192542810.193734882760.1572286130190.2383222989560.3264489038690.6552333043710.214276666395-0.361359116758-0.368152229328-0.354183441756-0.4098489025480.548709143213-0.2377644323310.3807429133670.03070881511120.1866511435130.7425461670220.1180638631130.429072763731-22.189066811720.3091056202-22.198391932
20.904501530033-0.1610357767370.2496876268970.890248935898-0.3175974095350.3323156458780.03836467416510.135612163317-0.0648599925561-0.173619935371-0.0869833400523-0.2068880172530.01603955152190.0717424882933-0.00242662176770.186399990293-0.04077074559510.04119711548850.2218006022670.01344805888520.216952550303-37.26013536529.5849194457-4.22144764227
30.8998183861220.2830670388580.08851549152790.567975889664-0.07412267842490.4492729760390.029947394278-0.1019249669850.09600914823020.0697165224535-0.05624764518320.0569705267924-0.0500225919765-0.05261420948282.42272561828E-50.163515177323-0.03207737795050.01237625141460.18362380478-0.03017085501490.142985153677-62.792002808641.30941638578.83156835651
40.417138647855-0.1805008671140.1071655597380.168762362086-0.2457674136760.396662828495-0.07023591141020.3408429502490.176616950305-0.270518138984-0.280997918290.696892449582-0.0955801479248-0.144573560046-0.4603918806930.2058028002990.0197695730423-0.2092607718310.329183242759-0.2334762605710.884737073547-95.70767769416.7521718628-0.667714000603
50.0317024169549-0.01270841755930.01663238425340.0556876435476-0.01674182849180.00896196399687-0.04958653832930.009277110033040.05427324735890.0327742723467-0.2720737176590.7125737485290.172845979085-0.270887311133-0.3249047864920.162124989349-0.1013557563420.01678047575020.437814646043-0.2879592052090.867484476894-96.475017569811.88451117526.37063127439
60.246458162739-0.0924670388167-0.0887852433860.3559556153670.1690775593820.0610546821328-0.0538900240166-0.0404998275748-0.09965846161440.14582426854-0.03004726533010.1550928213270.0351289144161-0.11635938350.0001352167139070.232925326031-0.05650295302440.02786780535220.2237973767410.01230713387320.215476539893-66.32771566234.6252378948312.388666891
70.2946957923320.0405800080312-0.09401532797390.9257926911580.3317347759610.272782145493-0.0131483460836-0.0414154834196-0.05925825524590.00954107950698-0.01933651811150.335434845302-0.0235541554285-0.0828626475803-0.001406265356720.201372596965-0.04891778040310.03230060806920.2604118101070.009148211978690.259906612554-75.975464267914.258084010611.8355641503
80.378861234650.131098083944-0.07450821857751.00943165851-0.01907365723420.5503868576860.0124626902373-0.060332221764-0.07236978423630.0615972358472-0.0326761701444-0.15762291890.03676733136860.0457038110807-2.591829187E-50.177836642205-0.03468548723430.002086592811060.1793228834140.02937060032930.215630459311-45.91824655790.5953428210318.07902231759
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 115 through 188 )AA115 - 1881 - 74
22chain 'A' and (resid 189 through 303 )AA189 - 30375 - 189
33chain 'A' and (resid 304 through 592 )AA304 - 592190 - 478
44chain 'B' and (resid 118 through 148 )BB118 - 1481 - 27
55chain 'B' and (resid 149 through 200 )BB149 - 20028 - 74
66chain 'B' and (resid 201 through 235 )BB201 - 23575 - 109
77chain 'B' and (resid 236 through 304 )BB236 - 304110 - 178
88chain 'B' and (resid 305 through 593 )BB305 - 593179 - 467

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