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- PDB-4zed: PBP AccA from A. tumefaciens C58 in complex with agrocinopine-3'-... -

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Basic information

Entry
Database: PDB / ID: 4zed
TitlePBP AccA from A. tumefaciens C58 in complex with agrocinopine-3'-O-benzoate
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
Chem-AGW / ABC transporter substrate-binding protein / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 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 1.1May 8, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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: ABC transporter, substrate binding protein (Agrocinopines A and B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8993
Polymers57,1781
Non-polymers7212
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint2 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.640, 114.920, 113.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 57178.102 Da / Num. of mol.: 1 / Fragment: UNP residues 30-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (strain C58 / ATCC 33970) (bacteria)
Gene: accA, Atu6139 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7D2F4, UniProt: Q52012*PLUS
#2: Chemical ChemComp-AGW / [(2S,3S,4R,5R)-2,5-bis(hydroxymethyl)-2-[(2R,3R,4R,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4-[oxidanyl-[(2R,3R,4S,5S)-2,4,5-tris(oxidanyl)oxan-3-yl]oxy-phosphoryl]oxy-oxolan-3-yl] benzoate


Mass: 658.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H35O19P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% P4K, 0.2M ACETATE NH4, 0.1M CITRATE NA PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
PH range: 5.6

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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: Feb 8, 2013
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 51499 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 11.5 % / Biso Wilson estimate: 28.67 Å2 / Rsym value: 0.092 / Net I/σ(I): 12.25
Reflection shellResolution: 1.75→1.85 Å / Rsym value: 0.844 / % possible all: 96.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTER2.10.0refinement
XDSdata scaling
RefinementResolution: 1.75→42.65 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.957 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.114 / SU Rfree Blow DPI: 0.099 / SU Rfree Cruickshank DPI: 0.097
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2571 5 %RANDOM
Rwork0.174 ---
obs0.175 51421 99.6 %-
Displacement parametersBiso mean: 29.73 Å2
Baniso -1Baniso -2Baniso -3
1--1.5518 Å20 Å20 Å2
2--0.1996 Å20 Å2
3---1.3522 Å2
Refine analyzeLuzzati coordinate error obs: 0.225 Å
Refinement stepCycle: LAST / Resolution: 1.75→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3944 0 48 414 4406
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094101HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.015574HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1390SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes100HARMONIC2
X-RAY DIFFRACTIONt_gen_planes581HARMONIC5
X-RAY DIFFRACTIONt_it4101HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.69
X-RAY DIFFRACTIONt_other_torsion16.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion513SEMIHARMONIC5
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_contact5101SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 187 4.99 %
Rwork0.2828 3560 -
all0.2845 3747 -
obs--99.58 %
Refinement TLS params.Method: refined / Origin x: -16.5043 Å / Origin y: -26.7053 Å / Origin z: 14.5401 Å
111213212223313233
T-0.0366 Å20.0009 Å2-0.0044 Å2--0.0687 Å20.0003 Å2---0.0698 Å2
L0.7794 °20.311 °2-0.0909 °2-0.8247 °2-0.0666 °2--0.3638 °2
S0.1002 Å °-0.0475 Å °0.0229 Å °0.1364 Å °-0.0449 Å °0.0197 Å °-0.0212 Å °0.0068 Å °-0.0554 Å °
Refinement TLS groupSelection details: A 32 A 521

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