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- PDB-8wch: Crystal structure of SAR11_0655 bound to a co-purified ligand, L-... -

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Basic information

Entry
Database: PDB / ID: 8wch
TitleCrystal structure of SAR11_0655 bound to a co-purified ligand, L-pyroglutamate
ComponentsProbable Leu/Ile/Val-binding protein
KeywordsTRANSPORT PROTEIN / ABC transporter / solute-binding protein / periplasmic binding protein
Function / homology: / Leucine-binding protein domain / Periplasmic binding protein / Periplasmic binding protein-like I / PYROGLUTAMIC ACID / Probable Leu/Ile/Val-binding protein
Function and homology information
Biological speciesCandidatus Pelagibacter ubique HTCC1062 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.519 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
DepositionSep 12, 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 Leu/Ile/Val-binding protein
B: Probable Leu/Ile/Val-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3466
Polymers90,0422
Non-polymers3044
Water10,845602
1
A: Probable Leu/Ile/Val-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1733
Polymers45,0211
Non-polymers1522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable Leu/Ile/Val-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1733
Polymers45,0211
Non-polymers1522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.204, 122.204, 125.908
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-767-

HOH

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Components

#1: Protein Probable Leu/Ile/Val-binding protein


Mass: 45020.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Pelagibacter ubique HTCC1062 (bacteria)
Strain: HTCC1062 / Gene: braC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4FMW4
#2: Chemical ChemComp-PCA / PYROGLUTAMIC ACID


Type: L-peptide linking / Mass: 129.114 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 2.74 Å3/Da / Density % sol: 55.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 1.5 uL 0.1 M sodium citrate pH 3.5, 0.15 M lithium sulfate, 16% (w/v) PEG 6000 + 1.5 uL 12 mg/mL protein. Cryoprotected in 0.1 M sodium citrate pH 3.5, 0.15 M lithium sulfate, 16% (w/v) PEG ...Details: 1.5 uL 0.1 M sodium citrate pH 3.5, 0.15 M lithium sulfate, 16% (w/v) PEG 6000 + 1.5 uL 12 mg/mL protein. Cryoprotected in 0.1 M sodium citrate pH 3.5, 0.15 M lithium sulfate, 16% (w/v) PEG 6000, 30% (v/v) ethylene glycol.

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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 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.519→43.846 Å / Num. obs: 146122 / % possible obs: 99.9 % / Redundancy: 20.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.136 / Net I/σ(I): 14.89
Reflection shellResolution: 1.52→1.61 Å / Rmerge(I) obs: 3.18 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 23258 / CC1/2: 0.506 / Rrim(I) all: 3.26 / % possible all: 99.6

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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: AlphaFold

Resolution: 1.519→41.304 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.174 / WRfactor Rwork: 0.143 / SU B: 3.128 / SU ML: 0.048 / Average fsc free: 0.97 / Average fsc work: 0.9784 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.063
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1867 7328 5.015 %
Rwork0.1502 138792 -
all0.152 --
obs-146120 99.917 %
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: 22.753 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å2-0 Å2
2---0.04 Å2-0 Å2
3---0.079 Å2
Refinement stepCycle: LAST / Resolution: 1.519→41.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5952 0 20 602 6574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126242
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165875
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.658479
X-RAY DIFFRACTIONr_angle_other_deg0.5651.5713596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0985823
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.518523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.877101036
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.28410251
X-RAY DIFFRACTIONr_chiral_restr0.0850.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027314
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021344
X-RAY DIFFRACTIONr_nbd_refined0.2260.21223
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.25217
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23122
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.23132
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2405
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0280.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3170.224
X-RAY DIFFRACTIONr_nbd_other0.2070.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2530.231
X-RAY DIFFRACTIONr_mcbond_it1.4642.2933209
X-RAY DIFFRACTIONr_mcbond_other1.4642.2933209
X-RAY DIFFRACTIONr_mcangle_it1.964.1374011
X-RAY DIFFRACTIONr_mcangle_other1.964.1374012
X-RAY DIFFRACTIONr_scbond_it1.8072.533033
X-RAY DIFFRACTIONr_scbond_other1.8072.533032
X-RAY DIFFRACTIONr_scangle_it2.3824.5154452
X-RAY DIFFRACTIONr_scangle_other2.3824.5144453
X-RAY DIFFRACTIONr_lrange_it3.03522.9677101
X-RAY DIFFRACTIONr_lrange_other2.73621.9216967
X-RAY DIFFRACTIONr_rigid_bond_restr3.788312117
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
1.519-1.5580.3295290.313100410.314106710.9160.92599.05350.299
1.558-1.6010.3025320.27599020.276104360.9340.94599.98080.258
1.601-1.6470.2564890.2396370.231101270.9560.96399.99010.208
1.647-1.6980.2364600.20994090.21198700.9640.9799.98990.183
1.698-1.7530.235000.1890240.18395240.9680.9791000.151
1.753-1.8150.1934790.14987490.15192280.9780.9861000.121
1.815-1.8830.1964320.1385310.13489660.9760.9999.96650.102
1.883-1.960.1944390.1281560.12385950.9790.9921000.094
1.96-2.0470.1644300.1178300.11382600.9850.9931000.087
2.047-2.1460.1733900.10975310.11279210.9830.9931000.089
2.146-2.2620.1663670.11571810.11775490.9840.99399.98680.095
2.262-2.3990.1453650.1167980.11171630.9870.9931000.093
2.399-2.5640.1563970.1163320.11367290.9860.9931000.098
2.564-2.7680.1632830.11859970.11962800.9870.9931000.108
2.768-3.0310.192550.13855720.1458270.9790.9891000.133
3.031-3.3870.2122750.16550110.16852860.9770.9851000.164
3.387-3.9060.1892520.16244440.16346960.9790.9881000.168
3.906-4.7740.1572100.1438110.14140210.9880.991000.159
4.774-6.7060.1861480.17930300.1831780.9830.9871000.213
6.706-41.3040.179960.18518060.18419030.9840.98299.94740.235

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