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- PDB-4zeb: PBP AccA from A. tumefaciens C58 in complex with agrocinopine A -

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Basic information

Entry
Database: PDB / ID: 4zeb
TitlePBP AccA from A. tumefaciens C58 in complex with agrocinopine A
ComponentsABC transporter, substrate binding protein (Agrocinopines A and B)
KeywordsTRANSPORT PROTEIN / PBP / CLASS C
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-L-arabinopyranose / DI(HYDROXYETHYL)ETHER / ABC transporter substrate-binding protein / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsEl Sahili, A. / Morera, S.
CitationJournal: Plos Pathog. / Year: 2015
Title: A Pyranose-2-Phosphate Motif Is Responsible for Both Antibiotic Import and Quorum-Sensing Regulation in Agrobacterium tumefaciens.
Authors: El Sahili, A. / Li, S.Z. / Lang, J. / Virus, C. / Planamente, S. / Ahmar, M. / Guimaraes, B.G. / Aumont-Nicaise, M. / Vigouroux, A. / Soulere, L. / Reader, J. / Queneau, Y. / Faure, D. / Morera, S.
History
DepositionApr 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _entity_src_gen.gene_src_strain / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Apr 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / pdbx_branch_scheme / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_branch_descriptor.descriptor / _pdbx_struct_assembly_gen.asym_id_list
Revision 3.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter, substrate binding protein (Agrocinopines A and B)
B: ABC transporter, substrate binding protein (Agrocinopines A and B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,6698
Polymers114,3562
Non-polymers1,3136
Water9,512528
1
A: ABC transporter, substrate binding protein (Agrocinopines A and B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8134
Polymers57,1781
Non-polymers6343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter, substrate binding protein (Agrocinopines A and B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8574
Polymers57,1781
Non-polymers6793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.210, 51.240, 119.950
Angle α, β, γ (deg.)90.00, 114.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ABC transporter, substrate binding protein (Agrocinopines A and B)


Mass: 57178.102 Da / Num. of mol.: 2 / Fragment: UNP residues 30-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (strain C58 / ATCC 33970) (bacteria)
Strain: C58 / ATCC 33970 / Gene: accA, Atu6139 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7D2F4, UniProt: Q52012*PLUS

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Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-D-gulopyranose-(1-2)-4-O-phosphono-beta-D-fructofuranose


Type: oligosaccharide / Mass: 422.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_4*OPO/3O/3=O][a2212h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Gulp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-ARA / alpha-L-arabinopyranose / alpha-L-arabinose / L-arabinose / arabinose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LArapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-arabinopyranoseCOMMON NAMEGMML 1.0
a-L-ArapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 530 molecules

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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.17 Å3/Da / Density % sol: 43.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 20K, 0.1M MES PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
PH range: 6.5

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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: Dec 13, 2012
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 78059 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 33.48 Å2 / Rsym value: 0.111 / Net I/σ(I): 7.87
Reflection shellResolution: 1.89→2.01 Å / Rsym value: 0.926 / % possible all: 95.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTER2.10.0refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OUP

4oup
PDB Unreleased entry


Resolution: 1.89→37.8 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2 3902 5 %RANDOM
Rwork0.172 ---
obs0.174 78050 98.7 %-
Displacement parametersBiso mean: 36.74 Å2
Baniso -1Baniso -2Baniso -3
1--6.338 Å20 Å2-0.057 Å2
2--0.2327 Å20 Å2
3---6.1053 Å2
Refine analyzeLuzzati coordinate error obs: 0.246 Å
Refinement stepCycle: LAST / Resolution: 1.89→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7886 0 83 528 8497
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018217HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0611177HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2805SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes202HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1170HARMONIC5
X-RAY DIFFRACTIONt_it8217HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.71
X-RAY DIFFRACTIONt_other_torsion16.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1031SEMIHARMONIC5
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_contact9892SEMIHARMONIC4
LS refinement shellResolution: 1.89→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3741 243 4.98 %
Rwork0.3116 4634 -
all0.3146 4877 -
obs--98.72 %
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)
10.51470.2804-0.39820.8021-0.54191.37580.0412-0.1036-0.00450.1012-0.1354-0.01220.02570.25520.0943-0.08390.02360.0236-0.0550.0268-0.0635.88516.080832.2491
21.19340.59120.47080.78280.1761.16010.0256-0.28640.1620.0889-0.1150.05310.0346-0.10320.0895-0.11930.01830.0069-0.0601-0.0521-0.0576.7638-5.749820.6917
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1A 32 A 521
2X-RAY DIFFRACTION2B 32 B 521

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