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- PDB-5org: Structure of the periplasmic binding protein (PBP) OccJ from A. t... -

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Basic information

Entry
Database: PDB / ID: 5org
TitleStructure of the periplasmic binding protein (PBP) OccJ from A. tumefaciens B6 in complex with octopine.
ComponentsOctopine-binding periplasmic protein
KeywordsOctopine-binding protein / Agrobacterium tumefaciens / Arginine / Bacterial Proteins / DNA / Bacterial / Gene Expression Regulation / Genes / Ligands / Plant Tumors / Plasmids
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 / ACETATE ION / Octopine-binding periplasmic protein
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. B6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Octopine-binding periplasmic protein
B: Octopine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,15442
Polymers55,9862
Non-polymers2,16940
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-186 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.490, 99.490, 157.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Octopine-binding periplasmic protein


Mass: 27992.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. B6 (bacteria)
Gene: occT, occJ / Production host: Escherichia coli (E. coli) / References: UniProt: P0A4F8

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Non-polymers , 7 types, 283 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-6DB / octopine


Mass: 246.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18N4O4
#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 3.48 Å3/Da / Density % sol: 64.69 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 4000, 0.1M Tris pH8.5, 0.1M 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: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. obs: 54705 / % possible obs: 99.6 % / Redundancy: 9.5 % / Biso Wilson estimate: 39.06 Å2 / Rsym value: 0.088 / Net I/σ(I): 14
Reflection shellResolution: 1.99→2.4 Å / Mean I/σ(I) obs: 1.7 / Num. unique all: 8556 / % possible all: 98.3

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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: 1.99→29.14 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.94 / Rfactor Rfree error: 0.01 / SU R Cruickshank DPI: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.131 / SU Rfree Blow DPI: 0.122 / SU Rfree Cruickshank DPI: 0.121
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2735 5 %RANDOM
Rwork0.196 ---
obs0.197 54686 99.7 %-
Displacement parametersBiso mean: 46.43 Å2
Baniso -1Baniso -2Baniso -3
1-2.5078 Å20 Å20 Å2
2--2.5078 Å20 Å2
3----5.0157 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: 1 / Resolution: 1.99→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 121 243 4138
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013925HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.125274HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1343SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes90HARMONIC2
X-RAY DIFFRACTIONt_gen_planes570HARMONIC5
X-RAY DIFFRACTIONt_it3925HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion16.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion525SEMIHARMONIC5
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_contact4865SEMIHARMONIC4
LS refinement shellResolution: 1.99→2.04 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 193 5.02 %
Rwork0.229 3652 -
all0.229 3845 -
obs--97.14 %
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)
13.2035-0.3016-0.41290.88470.48920.988-0.0657-0.4952-0.20590.21480.0979-0.01850.17270.1063-0.0322-0.25870.0491-0.0116-0.11190.0322-0.2044-15.5776-28.202122.7531
21.2465-0.72631.10291.0658-0.72932.35670.29040.1407-0.1317-0.2305-0.06770.03870.29440.4396-0.2227-0.21870.0745-0.0481-0.134-0.0889-0.19311.1463-37.2175-5.1618
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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