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- PDB-6hqh: Structure of Agrobacterium tumefaciens B6 strain PBP SocA complex... -

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Basic information

Entry
Database: PDB / ID: 6hqh
TitleStructure of Agrobacterium tumefaciens B6 strain PBP SocA complexed with Deoxyfructosylglutamine (DFG) at 1.8 A resolution
ComponentsMembrane-bound lytic murein transglycosylase F
KeywordsTRANSPORT PROTEIN / protein transport
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / periplasmic space / membrane
Similarity search - Function
Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Deoxyfructosylglutamine / Membrane-bound lytic murein transglycosylase F
Similarity search - Component
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsMorera, S. / Marty, L.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for High Specificity of Amadori Compound and Mannopine Opine Binding in Bacterial Pathogens.
Authors: Marty, L. / Vigouroux, A. / Aumont-Nicaise, M. / Dessaux, Y. / Faure, D. / Morera, S.
History
DepositionSep 25, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionOct 31, 2018ID: 5L9M
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane-bound lytic murein transglycosylase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5608
Polymers28,8791
Non-polymers6817
Water3,387188
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint15 kcal/mol
Surface area11070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.340, 63.690, 43.750
Angle α, β, γ (deg.)90.00, 104.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Membrane-bound lytic murein transglycosylase F


Mass: 28879.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: SY94_5601 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F4FYR3
#2: Chemical ChemComp-SNW / Deoxyfructosylglutamine / santhopine


Mass: 308.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N2O8
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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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: 1.88 Å3/Da / Density % sol: 34.62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: PEG 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→42.3 Å / Num. obs: 19258 / % possible obs: 94 % / Redundancy: 2.8 % / Biso Wilson estimate: 27 Å2 / Rsym value: 0.051 / Net I/σ(I): 12.9
Reflection shellResolution: 1.8→1.82 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5L9M

5l9m
PDB Unreleased entry


Resolution: 1.8→42.3 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.15 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.131
RfactorNum. reflection% reflectionSelection details
Rfree0.219 958 5 %RANDOM
Rwork0.183 ---
obs0.185 19152 96.6 %-
Displacement parametersBiso mean: 29.99 Å2
Baniso -1Baniso -2Baniso -3
1-2.1905 Å20 Å2-0.4812 Å2
2---4.372 Å20 Å2
3---2.1815 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 1.8→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 45 188 2059
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011914HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.972584HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d642SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes326HARMONIC5
X-RAY DIFFRACTIONt_it1914HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion16.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion245SEMIHARMONIC5
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_contact2362SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.82 Å / Total num. of bins used: 47
RfactorNum. reflection% reflection
Rfree0.4763 -4.9 %
Rwork0.3591 388 -
all0.3651 408 -
obs--85.59 %
Refinement TLS params.Method: refined / Origin x: 18.4379 Å / Origin y: 69.3733 Å / Origin z: -15.6905 Å
111213212223313233
T-0.1823 Å2-0.01 Å20.0163 Å2--0.2022 Å2-0.0135 Å2---0.0687 Å2
L1.9475 °20.0024 °2-0.2344 °2-1.7527 °20.2566 °2--0.9591 °2
S0.021 Å °-0.1393 Å °0.132 Å °0.0193 Å °-0.0347 Å °0.143 Å °0.0096 Å °-0.0085 Å °0.0138 Å °
Refinement TLS groupSelection details: { A|* }

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