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- PDB-4p0i: Structure of the PBP NocT -

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Basic information

Entry
Database: PDB / ID: 4p0i
TitleStructure of the PBP NocT
ComponentsNopaline-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / periplasmic binding protein
Function / homology
Function and homology information


nitrogen compound transport / 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
DI(HYDROXYETHYL)ETHER / Nopaline-binding periplasmic protein
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.89 Å
AuthorsVigouroux, A. / Morera, S.
Funding support France, 1items
OrganizationGrant numberCountry
ANRANR-12-BSV8-0003-01 France
CitationJournal: Plos Pathog. / Year: 2014
Title: Agrobacterium uses a unique ligand-binding mode for trapping opines and acquiring a competitive advantage in the niche construction on plant host.
Authors: Lang, J. / Vigouroux, A. / Planamente, S. / El Sahili, A. / Blin, P. / Aumont-Nicaise, M. / Dessaux, Y. / Morera, S. / Faure, D.
History
DepositionFeb 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Structure summary
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)58,9368
Polymers58,5192
Non-polymers4166
Water5,513306
1
A: Nopaline-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6146
Polymers29,2601
Non-polymers3545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nopaline-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3222
Polymers29,2601
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.860, 69.710, 74.380
Angle α, β, γ (deg.)90.00, 117.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nopaline-binding periplasmic protein


Mass: 29259.627 Da / Num. of mol.: 2 / Fragment: UNP residues 26-283
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / ATCC 33970 / Gene: nocT, Atu6027, AGR_pTi_67 / Production host: Escherichia coli (E. coli) / References: UniProt: P35120
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2M SA, 0.1 M Na citrate pH 5.6, 0.2M K tartrate, 5% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2010
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.89→38.8 Å / Num. obs: 43103 / % possible obs: 99.4 % / Redundancy: 6 % / Biso Wilson estimate: 29.32 Å2 / Net I/σ(I): 22.43

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 1.89→32.43 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.9202 / SU R Cruickshank DPI: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.158 / SU Rfree Blow DPI: 0.14 / SU Rfree Cruickshank DPI: 0.14
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 2151 5 %RANDOM
Rwork0.2049 ---
obs0.2065 43021 99.76 %-
Displacement parametersBiso mean: 39.48 Å2
Baniso -1Baniso -2Baniso -3
1--1.9336 Å20 Å2-2.1656 Å2
2---0.0558 Å20 Å2
3---1.9894 Å2
Refine analyzeLuzzati coordinate error obs: 0.344 Å
Refinement stepCycle: 1 / Resolution: 1.89→32.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3921 0 27 306 4254
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014017HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.065408HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1413SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes100HARMONIC2
X-RAY DIFFRACTIONt_gen_planes570HARMONIC5
X-RAY DIFFRACTIONt_it4017HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion539SEMIHARMONIC5
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_contact4864SEMIHARMONIC4
LS refinement shellResolution: 1.89→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3183 158 4.98 %
Rwork0.285 3015 -
all0.2867 3173 -
obs--99.76 %
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)
10.65550.59260.99131.95211.58864.44-0.0405-0.13590.02430.0734-0.24040.0036-0.1725-0.19190.2809-0.04310.0339-0.0198-0.02470.0102-0.06-31.7446-1.441-7.4669
21.3464-0.27440.57162.3941.30592.10650.05260.0871-0.0453-0.07490.1461-0.6470.03990.2416-0.1987-0.04110.03010.08030.0166-0.00970.2137-46.1347-17.575136.3389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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