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- PDB-5ore: Structure of the periplasmic binding protein (PBP) OccJ from agro... -

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Basic information

Entry
Database: PDB / ID: 5ore
TitleStructure of the periplasmic binding protein (PBP) OccJ from agrobacterium tumefaciens B6
ComponentsOctopine-binding periplasmic protein
KeywordsDNA / Agrobacterium tumefaciens / Arginine / Bacterial Proteins / 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-binding periplasmic protein
Similarity search - Component
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsVigouroux, A. / Morera, S.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BSV8-003-01/02/03 France
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 16, 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: Octopine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1615
Polymers27,9931
Non-polymers1684
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-21 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.300, 59.300, 125.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Octopine-binding periplasmic protein


Mass: 27992.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: occT, occJ / Production host: Escherichia coli (E. coli) / References: UniProt: P0A4F8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 1.98 Å3/Da / Density % sol: 37.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 4000, 0.1M Tris pH8.5, 0.2M acetate NH4

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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: Jun 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 271394 / % possible obs: 99.9 % / Redundancy: 14.3 % / Biso Wilson estimate: 66.86 Å2 / Rsym value: 0.14 / Net I/σ(I): 20.8
Reflection shellResolution: 2.35→2.49 Å / Mean I/σ(I) obs: 1.7 / Num. unique all: 1558 / Rsym value: 2.126 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4POW

4pow


Resolution: 2.35→43.18 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / Rfactor Rfree error: 0.001 / SU R Cruickshank DPI: 0.479 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.536 / SU Rfree Blow DPI: 0.264 / SU Rfree Cruickshank DPI: 0.262
RfactorNum. reflection% reflectionSelection details
Rfree0.251 498 5.01 %RANDOM
Rwork0.208 ---
obs0.21 9946 100 %-
Displacement parametersBiso mean: 68.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.7588 Å20 Å20 Å2
2--1.7588 Å20 Å2
3----3.5176 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.35→43.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 0 7 17 1970
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011993HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.262691HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d684SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes291HARMONIC5
X-RAY DIFFRACTIONt_it1993HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion22.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion267SEMIHARMONIC5
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_contact2270SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.63 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.239 137 4.99 %
Rwork0.226 2607 -
all0.226 2744 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 28.2574 Å / Origin y: 2.7614 Å / Origin z: -15.0227 Å
111213212223313233
T-0.4065 Å20.0192 Å20.0611 Å2--0.5025 Å20.001 Å2---0.4717 Å2
L4.9181 °21.9074 °2-0.0995 °2-3.2067 °20.5269 °2--2.3452 °2
S0.2761 Å °-0.0472 Å °0.3155 Å °0.0722 Å °-0.168 Å °0.182 Å °-0.1027 Å °0.1536 Å °-0.1081 Å °
Refinement TLS groupSelection details: { A|* }

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