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- PDB-4zek: PBP AccA from A. tumefaciens C58 in complex with L-arabinose-2-is... -

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Basic information

Entry
Database: PDB / ID: 4zek
TitlePBP AccA from A. tumefaciens C58 in complex with L-arabinose-2-isopropylphosphate
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-LAH / DI(HYDROXYETHYL)ETHER / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesAGROBACTERIUM TUMEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9077
Polymers57,1781
Non-polymers7296
Water3,639202
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint5 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.170, 114.060, 112.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein ABC TRANSPORTER, SUBSTRATE BINDING PROTEIN (AGROCINOPINES A AND B)


Mass: 57178.102 Da / Num. of mol.: 1 / Fragment: unp residues 29-527
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AGROBACTERIUM TUMEFACIENS (bacteria) / Gene: ACCA, ATU6139 / Production host: Escherichia coli (E. coli) / References: UniProt: Q52012*PLUS
#2: Sugar ChemComp-LAH / 2-O-[(R)-hydroxy(propan-2-yloxy)phosphoryl]-alpha-L-arabinopyranose / 2-O-[(R)-hydroxy(propan-2-yloxy)phosphoryl]-alpha-L-arabinose / 2-O-[(R)-hydroxy(propan-2-yloxy)phosphoryl]-L-arabinose / 2-O-[(R)-hydroxy(propan-2-yloxy)phosphoryl]-arabinose


Type: L-saccharide, alpha linking / Mass: 272.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17O8P

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Non-polymers , 4 types, 207 molecules

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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O4
#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.: 202 / 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: 43.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG 4K, 0.2M ACNH4, 0.1M NA CITRATE 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: Sep 29, 2013
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→42.23 Å / Num. obs: 29355 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 37.37 Å2 / Rsym value: 0.182 / Net I/σ(I): 7.88
Reflection shellResolution: 2.1→2.22 Å / Rsym value: 1.304 / % possible all: 96.6

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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: 2.09→42.2 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1468 5 %RANDOM
Rwork0.187 ---
obs0.19 29354 98.7 %-
Displacement parametersBiso mean: 40.08 Å2
Baniso -1Baniso -2Baniso -3
1-11.5498 Å20 Å20 Å2
2---10.7618 Å20 Å2
3----0.7879 Å2
Refine analyzeLuzzati coordinate error obs: 0.281 Å
Refinement stepCycle: LAST / Resolution: 2.09→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 47 202 4194
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094102HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.095560HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1413SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes101HARMONIC2
X-RAY DIFFRACTIONt_gen_planes582HARMONIC5
X-RAY DIFFRACTIONt_it4102HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion17.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion514SEMIHARMONIC5
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_contact4959SEMIHARMONIC4
LS refinement shellResolution: 2.09→2.16 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3005 126 5.01 %
Rwork0.2447 2391 -
all0.2473 2517 -
obs--98.65 %
Refinement TLS params.Method: refined / Origin x: -16.8244 Å / Origin y: -26.2477 Å / Origin z: 14.3479 Å
111213212223313233
T-0.1035 Å20.0201 Å20.0015 Å2-0.0344 Å2-0.0086 Å2---0.1067 Å2
L0.8839 °20.2147 °2-0.1505 °2-0.7231 °2-0.2239 °2--0.5036 °2
S0.0331 Å °0.0221 Å °0.0376 Å °0.0938 Å °0.0235 Å °0.013 Å °-0.0443 Å °0.0129 Å °-0.0566 Å °
Refinement TLS groupSelection details: A 32 A 521

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