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- PDB-5ito: Structure of the periplasmic binding protein M117N-NocT from A. t... -

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Basic information

Entry
Database: PDB / ID: 5ito
TitleStructure of the periplasmic binding protein M117N-NocT from A. tumefaciens in complex with octopine
ComponentsNopaline-binding periplasmic protein
KeywordsMEMBRANE PROTEIN / Periplasmic binding protein / opine / octopine
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Specific amino acids and opine-binding periplasmic protein, ABC transporter / Solute-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 / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...Specific amino acids and opine-binding periplasmic protein, ABC transporter / Solute-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 / 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
octopine / DI(HYDROXYETHYL)ETHER / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Nopaline-binding periplasmic protein
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsVigouroux, A. / Morera, S.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: ISME J / Year: 2017
Title: Fitness costs restrict niche expansion by generalist niche-constructing pathogens.
Authors: Lang, J. / Vigouroux, A. / El Sahili, A. / Kwasiborski, A. / Aumont-Nicaise, M. / Dessaux, Y. / Shykoff, J.A. / Morera, S. / Faure, D.
History
DepositionMar 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 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: Nopaline-binding periplasmic protein
B: Nopaline-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,83711
Polymers58,4852
Non-polymers1,3529
Water1,71195
1
A: Nopaline-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2247
Polymers29,2431
Non-polymers9816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nopaline-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6134
Polymers29,2431
Non-polymers3703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.590, 113.590, 37.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nopaline-binding periplasmic protein


Mass: 29242.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Gene: nocT, Atu6027, AGR_pTi_67 / Production host: Escherichia coli (E. coli) / References: UniProt: P35120

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Non-polymers , 6 types, 104 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-6DB / octopine


Mass: 246.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18N4O4
#6: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 4K, 0.1 M Tris pH8, 0.1 M LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→49 Å / Num. obs: 22829 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 56.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.7
Reflection shellResolution: 2.35→2.49 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.97 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4POX

4pox
PDB Unreleased entry


Resolution: 2.35→25.98 Å / Cor.coef. Fo:Fc: 0.9558 / Cor.coef. Fo:Fc free: 0.9397 / SU R Cruickshank DPI: 0.331 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.302 / SU Rfree Blow DPI: 0.198 / SU Rfree Cruickshank DPI: 0.206
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 1136 5 %RANDOM
Rwork0.1751 ---
obs0.1767 22711 99.97 %-
Displacement parametersBiso mean: 53.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.5132 Å20 Å20 Å2
2---0.5132 Å20 Å2
3---1.0264 Å2
Refine analyzeLuzzati coordinate error obs: 0.305 Å
Refinement stepCycle: LAST / Resolution: 2.35→25.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3915 0 91 95 4101
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014073HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.095473HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1434SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes101HARMONIC2
X-RAY DIFFRACTIONt_gen_planes576HARMONIC5
X-RAY DIFFRACTIONt_it4073HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion20.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion538SEMIHARMONIC5
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_contact4650SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.46 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2203 150 5.02 %
Rwork0.2024 2837 -
all0.2033 2987 -
obs--99.97 %
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)
11.16280.1840.00711.7650.53581.19570.03610.0567-0.12870.0379-0.03-0.10960.06130.0274-0.0062-0.1830.01630.0084-0.10170.0331-0.117520.4636-7.0926-3.179
22.98850.0136-0.31522.4783-0.08041.6808-0.0960.0261-0.3866-0.25120.0699-0.2853-0.21640.07770.0261-0.232-0.02360.1525-0.1060.0494-0.121554.9207-0.3128-14.3217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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