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- PDB-8hqr: Crystal structure of the arginine-/lysine-binding protein SAR11_1... -

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Basic information

Entry
Database: PDB / ID: 8hqr
TitleCrystal structure of the arginine-/lysine-binding protein SAR11_1210 from 'Candidatus Pelagibacter ubique' HTCC1062 bound to arginine
ComponentsABC transporter
KeywordsTRANSPORT PROTEIN / solute-binding protein / ABC transporter / periplasmic binding protein
Function / homologySolute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / ARGININE / ABC transporter
Function and homology information
Biological speciesCandidatus Pelagibacter ubique HTCC1062 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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
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: ABC transporter
B: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9184
Polymers59,5682
Non-polymers3502
Water10,413578
1
A: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9592
Polymers29,7841
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9592
Polymers29,7841
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.128, 84.689, 106.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC transporter


Mass: 29783.955 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Pelagibacter ubique HTCC1062 (bacteria)
Gene: occT, SAR11_1210 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4FLC2
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1 uL 12 mg/mL protein + 1 uL 21% (w/v) PEG 1500, 0.1 M MES pH 6.0. Final crystal obtained by serial microseeding from this condition. Crystal cryoprotected in 30% (w/v) PEG 1500, 0.1 M MES pH 6.0.

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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: Jul 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.32→47.4 Å / Num. obs: 121098 / % possible obs: 99.4 % / Redundancy: 12.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.123 / Rrim(I) all: 0.129 / Net I/σ(I): 10.44
Reflection shellResolution: 1.32→1.4 Å / Redundancy: 11.6 % / Rmerge(I) obs: 1.411 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 19320 / CC1/2: 0.709 / Rrim(I) all: 1.476 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSJan 10, 2022data reduction
XDSJan 10, 2022data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OT8

5ot8


Resolution: 1.32→47.4 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.26 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19047 6128 5.1 %RANDOM
Rwork0.1489 ---
obs0.15094 114968 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.203 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å20 Å2
2--3.6 Å2-0 Å2
3----2.19 Å2
Refinement stepCycle: 1 / Resolution: 1.32→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3865 0 24 578 4467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124101
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163900
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.6345573
X-RAY DIFFRACTIONr_angle_other_deg0.5631.5619104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7625575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.8651019
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90210731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2657
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024736
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02768
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.821.9992173
X-RAY DIFFRACTIONr_mcbond_other7.821.9992173
X-RAY DIFFRACTIONr_mcangle_it7.6333.0022722
X-RAY DIFFRACTIONr_mcangle_other7.6313.0012723
X-RAY DIFFRACTIONr_scbond_it7.6142.3831928
X-RAY DIFFRACTIONr_scbond_other7.6122.3821929
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1593.3762828
X-RAY DIFFRACTIONr_long_range_B_refined8.41235.1944595
X-RAY DIFFRACTIONr_long_range_B_other8.37630.6544416
X-RAY DIFFRACTIONr_rigid_bond_restr12.75138001
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.32→1.352 Å
RfactorNum. reflection% reflection
Rfree0.362 427 -
Rwork0.31 8281 -
obs--97.92 %

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