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- PDB-4ra1: PBP AccA from A. tumefaciens C58 in complex with D-Glucose-2-phosphate -

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Basic information

Entry
Database: PDB / ID: 4ra1
TitlePBP AccA from A. tumefaciens C58 in complex with D-Glucose-2-phosphate
ComponentsABC transporter, substrate binding protein (Agrocinopines A and B)
KeywordsTRANSPORT PROTEIN / Periplasmic binding protein C cluster
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
2-O-phosphono-alpha-D-glucopyranose / 2-O-phosphono-beta-D-glucopyranose / 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: 1.75 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
DepositionSep 9, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Structure summary
Revision 1.2Sep 2, 2015Group: Other
Revision 1.3Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: 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)58,0978
Polymers57,1781
Non-polymers9197
Water6,864381
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ABC transporter, substrate binding protein (Agrocinopines A and B)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)116,19416
Polymers114,3562
Non-polymers1,83714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area1920 Å2
ΔGint-14 kcal/mol
Surface area36830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.210, 113.870, 113.570
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 , 1 types, 1 molecules A

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


Mass: 57178.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (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, 2 molecules

#2: Sugar ChemComp-ALX / 2-O-phosphono-alpha-D-glucopyranose / 2-O-phosphono-alpha-D-glucose / 2-O-phosphono-D-glucose / 2-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp2PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Sugar ChemComp-BNX / 2-O-phosphono-beta-D-glucopyranose / 2-O-phosphono-beta-D-glucose / 2-O-phosphono-D-glucose / 2-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P

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Non-polymers , 3 types, 386 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsALX AND BNX ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.

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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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG 4K, 0.2M NH4 Acetate, 0.1M NaCitrate, pH 5.6 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2014
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 51001 / Num. obs: 50794 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 29.73 Å2
Reflection shellResolution: 1.75→1.85 Å / % possible all: 97.7

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Processing

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

4oux
PDB Unreleased entry


Resolution: 1.75→42.45 Å / Cor.coef. Fo:Fc: 0.9422 / Cor.coef. Fo:Fc free: 0.9314 / SU R Cruickshank DPI: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 2535 5 %RANDOM
Rwork0.1716 ---
all0.174 50794 --
obs0.1731 50684 99.95 %-
Displacement parametersBiso mean: 33.95 Å2
Baniso -1Baniso -2Baniso -3
1-4.7138 Å20 Å20 Å2
2---14.5642 Å20 Å2
3---9.8504 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.75→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 58 381 4384
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014107HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.035570HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1437SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes101HARMONIC2
X-RAY DIFFRACTIONt_gen_planes580HARMONIC5
X-RAY DIFFRACTIONt_it4107HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.87
X-RAY DIFFRACTIONt_other_torsion16.17
X-RAY DIFFRACTIONt_chiral_improper_torsion513SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5151SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3283 185 5.01 %
Rwork0.3081 3505 -
all0.3092 3690 -
obs--99.95 %
Refinement TLS params.Method: refined / Origin x: -16.5991 Å / Origin y: -26.3669 Å / Origin z: 14.5518 Å
111213212223313233
T-0.1256 Å20.032 Å2-0.0032 Å2--0.1157 Å2-0.013 Å2---0.1483 Å2
L1.0168 °20.279 °2-0.1243 °2-0.7344 °2-0.3136 °2--0.6474 °2
S0.068 Å °0.0834 Å °-0.0181 Å °0.1376 Å °0.0305 Å °0.011 Å °-0.0843 Å °-0.0203 Å °-0.0985 Å °
Refinement TLS groupSelection details: { A|32 - A|521 }

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