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- PDB-7z8e: Crystal structure of the substrate-binding protein YejA from S. m... -

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Basic information

Entry
Database: PDB / ID: 7z8e
TitleCrystal structure of the substrate-binding protein YejA from S. meliloti in complex with peptide fragment
Components
  • ABC transporter substrate-binding protein
  • GLY-SER-ASP-VAL-ALA
  • SER-SER
KeywordsTRANSPORT PROTEIN / Peptide transporter
Function / homologyPeptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space / ABC transporter substrate-binding protein
Function and homology information
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsMorera, S. / Vigouroux, V. / Travin, D.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mbio / Year: 2023
Title: Dual-Uptake Mode of the Antibiotic Phazolicin Prevents Resistance Acquisition by Gram-Negative Bacteria.
Authors: Travin, D.Y. / Jouan, R. / Vigouroux, A. / Inaba-Inoue, S. / Lachat, J. / Haq, F. / Timchenko, T. / Sutormin, D. / Dubiley, S. / Beis, K. / Morera, S. / Severinov, K. / Mergaert, P.
History
DepositionMar 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 3, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter substrate-binding protein
B: GLY-SER-ASP-VAL-ALA
D: SER-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,78410
Polymers70,1613
Non-polymers6237
Water10,593588
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint6 kcal/mol
Surface area25150 Å2
Unit cell
Length a, b, c (Å)59.900, 73.770, 140.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ABC transporter substrate-binding protein


Mass: 69521.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: CDO24_03695, CN211_22115, GHK53_10045, GHK55_21585 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A222JNH8

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Protein/peptide , 2 types, 2 molecules BD

#2: Protein/peptide GLY-SER-ASP-VAL-ALA


Mass: 447.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This is a fortuitous ligand of SmYejA originating from protein degradation or E.coli peptides
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide SER-SER


Mass: 192.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This is a fortuitous ligang of YejA / Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 595 molecules

#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8.5 / Details: 14% PEG 8K, 0.1 M Tris-HCl pH 8.5 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.58→65.35 Å / Num. obs: 86259 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.3
Reflection shellResolution: 1.58→1.67 Å / Rmerge(I) obs: 1.64 / Num. unique obs: 4780 / CC1/2: 0.54

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ICQ

5icq


Resolution: 1.58→65.35 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.096 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.091
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3629 4.92 %RANDOM
Rwork0.169 ---
obs0.17 73828 85.8 %-
Displacement parametersBiso max: 117.66 Å2 / Biso mean: 26.33 Å2 / Biso min: 11.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.7544 Å20 Å20 Å2
2---0.3101 Å20 Å2
3----0.4443 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.58→65.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4808 0 51 588 5447
Biso mean--45.25 35.55 -
Num. residues----595
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1734SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes867HARMONIC5
X-RAY DIFFRACTIONt_it5002HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion619SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6030SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5002HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6775HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion3.81
X-RAY DIFFRACTIONt_other_torsion14.92
LS refinement shellResolution: 1.58→1.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2617 76 5.15 %
Rwork0.2221 1401 -
all0.2242 1477 -
obs--14.16 %
Refinement TLS params.Method: refined / Origin x: -6.1444 Å / Origin y: -9.6429 Å / Origin z: 17.2749 Å
111213212223313233
T-0.0801 Å20.0178 Å2-0.0035 Å2--0.0908 Å2-0.0001 Å2---0.1001 Å2
L0.4182 °20.0968 °2-0.0668 °2-0.3001 °2-0.0925 °2--0.4529 °2
S0.005 Å °-0.0105 Å °0.0321 Å °0.0418 Å °0.0007 Å °0.0255 Å °-0.0513 Å °-0.0066 Å °-0.0056 Å °
Refinement TLS groupSelection details: { A|* }

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