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- PDB-7bay: Crystal structure of CbpF from Streptococcus pneumoniae complexed... -

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Basic information

Entry
Database: PDB / ID: 7bay
TitleCrystal structure of CbpF from Streptococcus pneumoniae complexed with a Ytterbium derivative
ComponentsCholine-binding protein F
KeywordsCHOLINE-BINDING PROTEIN
Function / homologyCholine-binding repeat / Putative cell wall binding repeat / Cell wall-binding repeat profile. / Cell wall/choline-binding repeat / CHOLINE ION / TRIETHYLENE GLYCOL / neutral Yb(III)-caged complex / Choline-binding protein F
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMartinez Caballero, S. / Hermoso, J.A.
CitationJournal: Acs Appl Bio Mater / Year: 2021
Title: First Lanthanide Complex for De Novo Phasing in Native Protein Crystallography at 1 angstrom Radiation
Authors: Prieto-Castaneda, A. / Martinez-Caballero, S. / Agarrabeitia, A.R. / Garcia-Moreno, I. / Moya, S.D.L. / Ortiz, M.J. / Hermoso, J.A.
History
DepositionDec 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Sep 2, 2026Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_nonpoly_atom_coordination
Item: _chem_comp.formula / _pdbx_entry_details.has_protein_modification
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Choline-binding protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,99712
Polymers36,3231
Non-polymers1,67411
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint39 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.904, 52.207, 73.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 1 molecules AA

#1: Protein Choline-binding protein F


Mass: 36322.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Strain: ATCC BAA-255 / R6 / Gene: cbpF, spr0337 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DR52

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Non-polymers , 5 types, 55 molecules

#2: Chemical
ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H14NO
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-T7K / neutral Yb(III)-caged complex / 8-[(4-hydroxyphenyl)methyl]-2,17,18-trioxa-5,8,11,14-tetraza-1(gamma)-ytterbatricyclo[9.6.3.25,14]docosane-3,16,19-trione / Yb(III) clathrochelate


Mass: 622.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N4O7Yb
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.05 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate PEG 8000 sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.65→47.53 Å / Num. obs: 13491 / % possible obs: 99.8 % / Redundancy: 8.4 % / Biso Wilson estimate: 55.52 Å2 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.035 / Net I/σ(I): 10.1
Reflection shellResolution: 2.65→2.78 Å / Rmerge(I) obs: 0.708 / Num. unique obs: 1761 / Rpim(I) all: 0.262

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V05

2v05


Resolution: 2.65→47.53 Å / SU ML: 0.3217 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1208
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2419 613 4.56 %
Rwork0.2008 12841 -
obs0.2028 13454 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.12 Å2
Refinement stepCycle: LAST / Resolution: 2.65→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 103 44 2727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00182763
X-RAY DIFFRACTIONf_angle_d0.39583744
X-RAY DIFFRACTIONf_chiral_restr0.0375337
X-RAY DIFFRACTIONf_plane_restr0.0016465
X-RAY DIFFRACTIONf_dihedral_angle_d11.4762396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.920.3341560.29413151X-RAY DIFFRACTION99.82
2.92-3.340.25851370.24833164X-RAY DIFFRACTION99.79
3.34-4.210.2361540.19173186X-RAY DIFFRACTION99.61
4.21-47.530.22041660.17033340X-RAY DIFFRACTION99.32
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)
12.23785835409-1.34993945386-1.37697368594.26901667494-1.182439390073.808879467620.3586554704450.525477827161.15709600483-0.517878826064-0.01906451238460.111340292414-0.4471023563770.0332372134873-0.3391676569870.5715537482360.05902458877420.1415237965990.4664182679260.1531853333720.7303171116589.4940372170645.2113281422-5.92439369001
24.02295527228-1.3224351578-0.451152561012.21324818707-0.6924252947823.157711470230.368197124406-0.0007212922075040.568920485155-0.1138187266310.004339046964350.230191279096-0.115601070272-0.0599191991079-0.3292731778170.315933835301-0.01702563722410.02276632340680.3136210780970.01890961264460.49862892950411.423707707135.4319400377-0.286646393142
32.121313414720.616832675664-0.3507735826480.548386749742-0.1007637546650.9608280403510.2553123623980.08303364956820.5529253615110.320439465128-0.1277546190140.00677753897027-0.186942114515-0.111677860898-0.02079445994650.4502069073360.04932033593020.1358353808830.5180951504080.021729939910.465581148222-0.36403639920535.77324422313.1089504024
43.10120015965-0.614476805285-1.083457033822.46798883593-2.136487881114.089320020740.02669012225590.3694666346280.6006756693060.062241012648-0.0723302566921-0.384502832081-0.0667474152410.3684103867450.1026951602980.3248135502630.02837990354330.06281648283180.4101020826390.07398322803380.43843206468719.891310584930.18490088252.68525366625
51.36614251989-0.7570949924770.6990102024782.96796219368-1.654633641284.105137964310.372680177082-0.02023059880110.00964244115886-0.129666311162-0.275499480604-0.430749390441-0.0284314219410.00520692301552-0.06869042393730.2756443512530.03917239558480.005383536981330.3544975173120.05375839960080.31647324976819.158759935716.45653262686.95018713602
61.39575516660.4336599008050.3143730148351.34538490602-0.6314510762650.492828280904-0.268576546094-0.2334266685190.4242210878210.5617407728840.4958584380390.0265985634456-0.571008705380.0874824605725-0.2178210604120.5109466177010.0375969621931-0.05185736239970.5702597391430.03278233617280.43797630897417.360503064621.562933901719.9587543899
71.176196605971.008506664721.01014374843.072957238970.2024245699163.119134015320.142646355005-0.296864018168-0.278587774560.0664511703748-0.0575784820110.640734691169-0.376125720205-0.267610621457-0.1530854852690.4301177157610.02312410282210.05949101276480.506543855130.06430141365810.33249728460213.366460679710.59984580819.1779967436
80.348543269688-0.00520677145615-0.137896277073.08442519611-2.340257041732.389035077860.0579574964920.07554936851940.0797558619467-0.0945642064920.1579851751940.09001608731810.0601245908509-0.0715613598353-0.2045974513740.331886571218-0.0237179987759-0.01806010891280.4557630328780.04844242776090.35403320523618.1255500118-8.5918914322634.4104698189
91.67892771456-0.9908364556751.75304355491.44552669332-2.485090696744.49278134104-0.243780542360.338138777046-0.145925769762-0.4594592429280.5109216511790.5370305885210.863228899569-0.938387765465-0.08894084769920.470815619214-0.05245019561510.005515760101050.5887399223830.1518308344170.5712232203649.93030581428-24.480844174846.0934650454
103.28763901506-1.296236650512.796170618374.487626162080.2085091272975.47430286242-0.142245868673-0.53912204914-0.7631086414140.774784834309-0.00366037496888-0.1929320252371.019563378480.1184221888220.0003686141526860.5817959096090.1024260967880.1554104729750.6501786013230.1150083666150.53271333686814.9205281874-28.49337912955.9332980661
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: AA / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'AA' and (resid 1 through 25 )1 - 251 - 25
22chain 'AA' and (resid 26 through 50 )26 - 5026 - 50
33chain 'AA' and (resid 51 through 72 )51 - 7251 - 72
44chain 'AA' and (resid 73 through 109 )73 - 10973 - 109
55chain 'AA' and (resid 110 through 144 )110 - 144110 - 144
66chain 'AA' and (resid 145 through 165 )145 - 165145 - 165
77chain 'AA' and (resid 166 through 193 )166 - 193166 - 193
88chain 'AA' and (resid 194 through 265 )194 - 265194 - 265
99chain 'AA' and (resid 266 through 286 )266 - 286266 - 286
1010chain 'AA' and (resid 287 through 311 )287 - 311287 - 311

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