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- PDB-5ot8: Structure of the periplasmic binding protein (PBP) NocT-G97S muta... -

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Basic information

Entry
Database: PDB / ID: 5ot8
TitleStructure of the periplasmic binding protein (PBP) NocT-G97S mutant from A. tumefaciens C58 in complex with octopine.
ComponentsNopaline-binding periplasmic protein
KeywordsPROTEIN BINDING / Agrobacterium tumefaciens / Arginine / Bacterial Proteins / DNA / Bacterial / Gene Expression Regulation / Genes / Ligands / Plant Tumors / Plasmids
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
octopine / DI(HYDROXYETHYL)ETHER / Nopaline-binding periplasmic protein
Similarity search - Component
Biological speciesAgrobacterium fabrum str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsVigouroux, A. / Morera, S.
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis for high specificity of octopine binding in the plant pathogen Agrobacterium tumefaciens.
Authors: Vigouroux, A. / El Sahili, A. / Lang, J. / Aumont-Nicaise, M. / Dessaux, Y. / Faure, D. / Morera, S.
History
DepositionAug 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 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)59,77918
Polymers58,5792
Non-polymers1,20016
Water91951
1
A: Nopaline-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,17214
Polymers29,2901
Non-polymers88313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nopaline-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6074
Polymers29,2901
Non-polymers3173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.720, 115.720, 38.030
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: 29289.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HHHHHH : Tag
Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria)
Gene: nocT, Atu6027, AGR_pTi_67 / Production host: Escherichia coli (E. coli) / References: UniProt: P35120

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Non-polymers , 6 types, 67 molecules

#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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
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: 1.006 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 23735 / % possible obs: 99.8 % / Redundancy: 10.5 % / Biso Wilson estimate: 57.87 Å2 / Rsym value: 0.093 / Net I/σ(I): 11.6
Reflection shellResolution: 2.35→2.49 Å / Mean I/σ(I) obs: 1.8 / Num. unique all: 3814 / Rsym value: 0.715 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ITP

5itp


Resolution: 2.35→26.43 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.948 / Rfactor Rfree error: 0.001 / SU R Cruickshank DPI: 0.314 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.284 / SU Rfree Blow DPI: 0.19 / SU Rfree Cruickshank DPI: 0.198
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1184 5 %RANDOM
Rwork0.182 ---
obs0.183 23672 99.9 %-
Displacement parametersBiso mean: 52.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.9517 Å20 Å20 Å2
2--0.9517 Å20 Å2
3----1.9035 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 2.35→26.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3928 0 67 51 4046
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014061HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.095471HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1423SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes579HARMONIC5
X-RAY DIFFRACTIONt_it4061HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion19.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion546SEMIHARMONIC5
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_contact4477SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.45 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.25 144 5 %
Rwork0.213 2735 -
all0.215 2879 -
obs--100 %
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)
11.5676-0.3819-0.46541.40540.14791.3210.07620.04550.08860.0428-0.04190.0591-0.0726-0.0608-0.0343-0.1568-0.0207-0.0094-0.2091-0.0032-0.1494.098821.6137-11.228
22.8956-0.1991-0.27812.38430.46241.936-0.0209-0.24950.22450.13280.00520.10880.02330.25980.0157-0.1743-0.1291-0.0218-0.183-0.0569-0.301927.434648.1750.4719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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