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- PDB-5itp: Structure of the periplasmic binding protein NocT from A.tumefaci... -

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Basic information

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


nitrogen compound transport / ligand-gated 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 / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Ionotropic glutamate receptor / 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 / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Ionotropic glutamate receptor / 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 / Nopaline-binding periplasmic protein
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization

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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)59,55212
Polymers58,5192
Non-polymers1,03310
Water4,630257
1
A: Nopaline-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,04610
Polymers29,2601
Non-polymers7879
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nopaline-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5062
Polymers29,2601
Non-polymers2461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.640, 114.640, 38.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Nopaline-binding periplasmic protein


Mass: 29259.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (bacteria) / Gene: nocT, Atu6027, AGR_pTi_67 / Production host: Escherichia coli (E. coli) / References: UniProt: P35120
#2: Chemical ChemComp-6DB / octopine / Octopine


Mass: 246.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18N4O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 4K, 100 mM Tris pH 8.5 and 0.1 mM 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: Nov 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→49 Å / Num. obs: 47709 / % possible obs: 99.6 % / Redundancy: 5 % / Biso Wilson estimate: 34.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 14
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.4 / % possible all: 97.9

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4POX
Resolution: 1.85→27.09 Å / Cor.coef. Fo:Fc: 0.9641 / Cor.coef. Fo:Fc free: 0.958 / SU R Cruickshank DPI: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.119 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.107
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2383 5 %RANDOM
Rwork0.1768 ---
obs0.1778 47656 99.75 %-
Displacement parametersBiso mean: 41.23 Å2
Baniso -1Baniso -2Baniso -3
1-1.0485 Å20 Å20 Å2
2--1.0485 Å20 Å2
3----2.097 Å2
Refine analyzeLuzzati coordinate error obs: 0.258 Å
Refinement stepCycle: 1 / Resolution: 1.85→27.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3901 0 69 257 4227
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014037HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.025432HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1410SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes576HARMONIC5
X-RAY DIFFRACTIONt_it4037HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion17.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion537SEMIHARMONIC5
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_contact4970SEMIHARMONIC4
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2752 172 5.01 %
Rwork0.2629 3263 -
all0.2635 3435 -
obs--99.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.03990.0485-0.441.3186-0.33511.0678-0.0191-0.00290.04220.0550.07810.215-0.0228-0.1302-0.0591-0.09220.039-0.0131-0.0764-0.0006-0.0599-16.387780.48250.1882
22.0627-0.0697-0.21291.98680.19791.3840.036-0.1438-0.04680.1035-0.09590.1491-0.13780.17980.0599-0.00980.10420.0097-0.144-0.0453-0.1515-27.9054113.544411.8312
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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