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- PDB-8hqq: Crystal structure of the glucose-binding protein SAR11_0769 from ... -

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Basic information

Entry
Database: PDB / ID: 8hqq
TitleCrystal structure of the glucose-binding protein SAR11_0769 from "Candidatus Pelagibacter ubique" HTCC1062 bound to glucose
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-glucopyranose / Probable sugar-binding periplasmic protein
Function and homology information
Biological speciesCandidatus Pelagibacter ubique HTCC1062 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsClifton, B.E. / Laurino, P.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other private Japan
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
DepositionDec 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: 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
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.642, 44.642, 329.112
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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)
Gene: SAR11_0769 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: Q4FMK2
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


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
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1 uL 12 mg/mL protein + 1 uL 18.5% (w/v) PEG 1500, 10% (v/v) isopropanol, 0.1 M Bis-Tris pH 6.5. Crystal was cryoprotected in 15% (w/v) PEG 1500, 30% (v/v) ethylene glycol, 10% (v/v) ...Details: 1 uL 12 mg/mL protein + 1 uL 18.5% (w/v) PEG 1500, 10% (v/v) isopropanol, 0.1 M Bis-Tris pH 6.5. Crystal was cryoprotected in 15% (w/v) PEG 1500, 30% (v/v) ethylene glycol, 10% (v/v) isopropanol, 0.1 M Bis-Tris pH 6.5.

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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: Oct 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→47.02 Å / Num. obs: 33089 / % possible obs: 99 % / Redundancy: 12 % / CC1/2: 0.986 / Rmerge(I) obs: 0.239 / Rrim(I) all: 0.248 / Net I/σ(I): 6.28
Reflection shellResolution: 1.86→1.98 Å / Redundancy: 9.49 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 4941 / CC1/2: 0.913 / Rrim(I) all: 0.545 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PHENIX1.20.1-4487-000refinement
XDSJan 10, 2022data reduction
XDSJan 10, 2022data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.86→38.4 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.36 / Stereochemistry target values: ML
Details: Initial refinement by simulated annealing in Phenix, followed by iterative real-space and reciprocal-space refinement in COOT and Refmac. Final rounds of reciprocal-space refinement ...Details: Initial refinement by simulated annealing in Phenix, followed by iterative real-space and reciprocal-space refinement in COOT and Refmac. Final rounds of reciprocal-space refinement including TLS refinement were performed in Phenix.
RfactorNum. reflection% reflection
Rfree0.2369 1608 4.87 %
Rwork0.2037 --
obs0.2054 33030 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 12 99 3071
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.931
X-RAY DIFFRACTIONf_dihedral_angle_d6.348
X-RAY DIFFRACTIONf_chiral_restr0.054
X-RAY DIFFRACTIONf_plane_restr0.008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.920.3913970.3332543X-RAY DIFFRACTION90
1.92-1.990.38011290.29562772X-RAY DIFFRACTION98
1.99-2.070.30471270.26722824X-RAY DIFFRACTION99
2.07-2.170.28411340.24012819X-RAY DIFFRACTION100
2.17-2.280.29861650.22752832X-RAY DIFFRACTION100
2.28-2.420.23391280.22962873X-RAY DIFFRACTION100
2.42-2.610.27061460.21922879X-RAY DIFFRACTION100
2.61-2.870.26031590.20922877X-RAY DIFFRACTION100
2.87-3.290.23611470.20862910X-RAY DIFFRACTION100
3.29-4.140.21851620.1762959X-RAY DIFFRACTION100
4.14-38.40.19142140.16783134X-RAY DIFFRACTION100
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)
10.673-0.4124-0.1260.47880.2030.18090.1704-0.17140.37420.4978-0.13190.4982-0.0909-0.2614-0.03970.4196-0.12490.1440.458-0.09530.3825-20.88558.0377-15.8174
21.36070.2926-0.16241.8404-0.63641.70860.2385-0.29440.42920.4758-0.17130.1349-0.5424-0.0282-0.130.4337-0.07860.1110.3267-0.05870.3301-10.102417.2134-16.7316
31.2762-0.3078-0.1741.80610.57031.69620.3591-0.56980.06520.8867-0.3244-0.183-0.01520.1068-0.09020.6283-0.2282-0.02190.5114-0.01360.3104-3.49414.8033-6.8018
40.76050.53660.14611.08630.21772.08180.00030.03320.0180.05060.08830.0160.08930.0917-0.07860.2625-0.0570.01690.2415-0.00420.2537-7.4212-1.4809-36.5917
51.69140.63230.06441.17870.05711.36980.00130.0575-0.0601-0.02090.0508-0.0250.04930.1534-0.05440.2473-0.05750.01290.27720.01070.2320.12525.7771-38.3367
61.59350.5336-0.05561.32250.43721.61910.1418-0.18390.02610.4143-0.14440.13470.1921-0.260.03070.3976-0.11350.05610.28840.00730.2567-13.2264-0.8041-22.4091
71.74580.0612-0.06991.0287-0.45361.0940.09740.102-0.18950.3051-0.1103-0.1280.13860.02480.01450.3582-0.078-0.00320.3179-0.01640.2564-1.1477-3.3761-25.4221
80.5677-0.21180.56080.68670.39271.31550.09220.23210.0708-0.0130.00660.079-0.2160.0224-0.10610.2781-0.12820.02750.29610.02040.25935.710415.654-37.6393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 126 )
4X-RAY DIFFRACTION4chain 'A' and (resid 127 through 188 )
5X-RAY DIFFRACTION5chain 'A' and (resid 189 through 257 )
6X-RAY DIFFRACTION6chain 'A' and (resid 258 through 352 )
7X-RAY DIFFRACTION7chain 'A' and (resid 353 through 382 )
8X-RAY DIFFRACTION8chain 'A' and (resid 383 through 418 )

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