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- PDB-8kd0: Crystal structure of SAR11_0769 from 'Candidatus Pelagibacter ubi... -

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Basic information

Entry
Database: PDB / ID: 8kd0
TitleCrystal structure of SAR11_0769 from 'Candidatus Pelagibacter ubique' HTCC1062 bound to a co-purified ligand, beta-galactopyranose
ComponentsProbable binding protein component of ABC sugar transporter
KeywordsTRANSPORT PROTEIN / ABC transporter / glucose transporter / periplasmic binding protein / solute-binding protein
Function / homology: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / beta-D-galactopyranose / Probable sugar-binding periplasmic protein
Function and homology information
Biological speciesCandidatus Pelagibacter ubique HTCC1062 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.675 Å
AuthorsClifton, B.E. / Laurino, P.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nature / Year: 2024
Title: The ultra-high affinity transport proteins of ubiquitous marine bacteria.
Authors: Clifton, B.E. / Alcolombri, U. / Uechi, G.I. / Jackson, C.J. / Laurino, P.
History
DepositionAug 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: 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.title / _citation.year
Revision 1.2Sep 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 30, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable binding protein component of ABC sugar transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1062
Polymers44,9261
Non-polymers1801
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.879, 43.879, 328.555
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Probable binding protein component of ABC sugar transporter


Mass: 44926.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Pelagibacter ubique HTCC1062 (bacteria)
Strain: HTCC1062 / Gene: SAR11_0769 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express / References: UniProt: Q4FMK2
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 20% (v/v) 2-propanol, 0.1 M MES pH 6.5, 23% (w/v) PEG 1500. 1.2 uL protein + 1.2 uL precipitant.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→46.936 Å / Num. obs: 43960 / % possible obs: 99.6 % / Redundancy: 12.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.135 / Rrim(I) all: 0.141 / Net I/σ(I): 11.08
Reflection shellResolution: 1.67→1.78 Å / Redundancy: 11.37 % / Rmerge(I) obs: 1.608 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 6771 / CC1/2: 0.864 / Rrim(I) all: 1.683 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSJun 30, 2023data reduction
XDSJun 30, 2023data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8HQQ

8hqq


Resolution: 1.675→38.029 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.197 / SU B: 7.858 / SU ML: 0.106 / Average fsc free: 0.9499 / Average fsc work: 0.9563 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.105
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2288 2217 5.044 %
Rwork0.1937 41733 -
all0.195 --
obs-43950 99.547 %
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: 40.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.066 Å20.533 Å2-0 Å2
2--1.066 Å20 Å2
3----3.457 Å2
Refinement stepCycle: LAST / Resolution: 1.675→38.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 12 81 3026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123035
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162791
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.6284128
X-RAY DIFFRACTIONr_angle_other_deg0.4841.5736421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2525404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.32857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65310466
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.73310128
X-RAY DIFFRACTIONr_chiral_restr0.0670.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02682
X-RAY DIFFRACTIONr_nbd_refined0.2150.2649
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.22476
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21548
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21596
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2104
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.25
X-RAY DIFFRACTIONr_nbd_other0.1390.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.26
X-RAY DIFFRACTIONr_mcbond_it1.8642.621595
X-RAY DIFFRACTIONr_mcbond_other1.8572.621595
X-RAY DIFFRACTIONr_mcangle_it2.3684.6991994
X-RAY DIFFRACTIONr_mcangle_other2.3684.71995
X-RAY DIFFRACTIONr_scbond_it2.6642.851440
X-RAY DIFFRACTIONr_scbond_other2.6632.8491441
X-RAY DIFFRACTIONr_scangle_it3.9095.1262130
X-RAY DIFFRACTIONr_scangle_other3.9085.1252131
X-RAY DIFFRACTIONr_lrange_it4.40424.9643471
X-RAY DIFFRACTIONr_lrange_other4.40124.9273462
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
1.675-1.7180.3551420.32928360.33131650.8730.88694.09160.322
1.718-1.7650.3111630.31929750.31831380.8940.8931000.306
1.765-1.8160.291630.29428770.29430410.9340.92199.96710.276
1.816-1.8720.284970.2528070.25129050.9390.94999.96560.228
1.872-1.9330.2351470.24727180.24628670.9580.95299.93020.221
1.933-2.0010.2441730.21826500.2228250.9530.96399.92920.189
2.001-2.0760.271260.20924890.21126160.9540.96999.96180.182
2.076-2.1610.2071310.18624370.18725680.9720.9761000.163
2.161-2.2570.2541390.223290.20324700.9570.97399.9190.178
2.257-2.3660.2291400.19222710.19424110.9690.9771000.173
2.366-2.4940.2231090.18521330.18722420.9670.9781000.171
2.494-2.6440.211000.17620840.17821840.9640.9811000.164
2.644-2.8260.237840.19419660.19620500.9630.9761000.189
2.826-3.0510.2361170.20617950.20819120.9650.9731000.205
3.051-3.340.262890.21516810.21717700.9610.9711000.217
3.34-3.7310.222860.19215330.19416190.9760.9791000.205
3.731-4.3010.194720.15813890.15914610.9740.9851000.178
4.301-5.2510.17480.14611930.14712430.9840.98799.83910.174
5.251-7.3560.252540.1869670.18910210.9730.9821000.227
7.356-38.0290.195370.1886030.1886400.9740.9791000.255
Refinement TLS params.Method: refined / Origin x: 0.229 Å / Origin y: 8.0484 Å / Origin z: 28.2114 Å
111213212223313233
T0.0342 Å2-0.0061 Å20.0121 Å2-0.0236 Å20.0067 Å2--0.0542 Å2
L0.9646 °2-0.0956 °2-0.1493 °2-0.6417 °20.3177 °2--5.5189 °2
S-0.0269 Å °-0.1086 Å °0.005 Å °0.1386 Å °-0.0348 Å °0.0371 Å °0.1188 Å °-0.1703 Å °0.0617 Å °
Refinement TLS groupSelection: ALL

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