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- PDB-5l9s: Structure of Agrobacterium tumefaciens C58 strain PBP AttC in ope... -

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Basic information

Entry
Database: PDB / ID: 5l9s
TitleStructure of Agrobacterium tumefaciens C58 strain PBP AttC in open unliganded conformation
ComponentsABC transporter, substrate binding protein (Mannopine)
KeywordsTRANSPORT PROTEIN / periplasmic binding protein ABC transporter
Function / homology
Function and homology information


thiamine binding / thiamine transport / thiamine pyrophosphate binding / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ABC transporter, substrate binding protein (Mannopine)
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsMarty, L. / Morera, S.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for High Specificity of Amadori Compound and Mannopine Opine Binding in Bacterial Pathogens.
Authors: Marty, L. / Vigouroux, A. / Aumont-Nicaise, M. / Dessaux, Y. / Faure, D. / Morera, S.
History
DepositionJun 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,6714
Polymers74,5502
Non-polymers1212
Water1,72996
1
A: ABC transporter, substrate binding protein (Mannopine)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3342
Polymers37,2751
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter, substrate binding protein (Mannopine)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3372
Polymers37,2751
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.010, 118.450, 121.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC transporter, substrate binding protein (Mannopine)


Mass: 37275.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Gene: attC, Atu5129 / Production host: Escherichia coli (E. coli) / References: UniProt: A9CLM6
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#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.: 96 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 40% PEG 4K, 0.1M MES pH 6.5, 0.2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 24641 / % possible obs: 99 % / Redundancy: 5.1 % / Biso Wilson estimate: 64.25 Å2 / Rsym value: 0.115 / Net I/σ(I): 11.57
Reflection shellResolution: 2.49→2.64 Å / Rsym value: 1.259

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L9G

5l9g


Resolution: 2.49→28.59 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.928 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.564 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.589 / SU Rfree Blow DPI: 0.263 / SU Rfree Cruickshank DPI: 0.266
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1230 5 %RANDOM
Rwork0.19 ---
obs0.192 24601 98.7 %-
Displacement parametersBiso mean: 65.75 Å2
Baniso -1Baniso -2Baniso -3
1-6.1241 Å20 Å20 Å2
2--6.0982 Å20 Å2
3----12.2223 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.49→28.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5122 0 8 96 5226
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015244HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.157123HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1805SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes138HARMONIC2
X-RAY DIFFRACTIONt_gen_planes760HARMONIC5
X-RAY DIFFRACTIONt_it5244HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion21.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion681SEMIHARMONIC5
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_contact5837SEMIHARMONIC4
LS refinement shellResolution: 2.49→2.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.333 135 4.98 %
Rwork0.248 2575 -
all0.252 2710 -
obs--90.99 %
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)
11.661-0.18070.4114.22290.02883.0632-0.0951-0.0415-0.13080.490.12530.1259-0.24510.0893-0.0301-0.1052-0.00930.0235-0.1323-0.0286-0.320537.980131.746324.6936
22.0162-2.8044-0.15454.35750.80020.9121-0.09040.2052-0.70790.3334-0.20321.01940.2589-0.11730.2936-0.2023-0.0550.1096-0.1602-0.1160.071437.0779-2.91944.8019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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