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- PDB-6hlz: Structure in C2 form of the PBP AgtB from A.tumefacien R10 in com... -

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Basic information

Entry
Database: PDB / ID: 6hlz
TitleStructure in C2 form of the PBP AgtB from A.tumefacien R10 in complex with agropinic acid
ComponentsAgropine permease
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / ABC transporter
Function / homologyPeriplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / agropinic acid / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesAgrobacterium tumefaciens LBA4213
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsMorera, S. / Marty, L. / Vigouroux, A.
CitationJournal: Biochem. J. / Year: 2019
Title: Structural basis for two efficient modes of agropinic acid opine import into the bacterial pathogenAgrobacterium tumefaciens.
Authors: Marty, L. / Vigouroux, A. / Aumont-Nicaise, M. / Pelissier, F. / Meyer, T. / Lavire, C. / Dessaux, Y. / Morera, S.
History
DepositionSep 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Agropine permease
B: Agropine permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,53368
Polymers74,5842
Non-polymers5,94966
Water11,169620
1
A: Agropine permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,04543
Polymers37,2921
Non-polymers3,75342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Agropine permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,48725
Polymers37,2921
Non-polymers2,19624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.830, 40.930, 117.420
Angle α, β, γ (deg.)90.00, 115.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-551-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Agropine permease


Mass: 37291.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens LBA4213 (Ach5) (bacteria)
Gene: agtB, X971_5368 / Production host: Escherichia coli (E. coli) / References: UniProt: W8FRA6

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Non-polymers , 6 types, 686 molecules

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


Mass: 62.068 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O3
#4: Chemical ChemComp-G9Z / agropinic acid


Mass: 291.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17NO8
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 8K, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 58982 / % possible obs: 98.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 36.1 Å2 / Rsym value: 0.149 / Net I/σ(I): 7
Reflection shellResolution: 1.89→2 Å / Rsym value: 0.933

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L9G

5l9g


Resolution: 1.89→42.61 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.169 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2949 5 %RANDOM
Rwork0.206 ---
obs0.208 58975 99.1 %-
Displacement parametersBiso mean: 36.73 Å2
Baniso -1Baniso -2Baniso -3
1-6.1294 Å20 Å23.4305 Å2
2---2.1284 Å20 Å2
3----4.001 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 1.89→42.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 392 620 5870
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015310HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.067064HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1789SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes848HARMONIC5
X-RAY DIFFRACTIONt_it5310HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion17.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion648SEMIHARMONIC5
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_contact6448SEMIHARMONIC4
LS refinement shellResolution: 1.89→1.91 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3752 -5 %
Rwork0.3463 1121 -
all0.3477 1180 -
obs--72.13 %
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)
10.64380.15980.39650.54120.07170.43030.01450.0347-0.0014-0.0396-0.00630.0511-0.00930.0042-0.0082-0.21660.01160.0184-0.0891-0.0023-0.206726.1113-20.487-17.6774
20.5961-0.15960.11780.47150.05561.4001-0.0172-0.1011-0.02420.04620.028-0.02050.0211-0.0199-0.0108-0.22710.00260.024-0.0836-0.0072-0.225516.6916-32.903522.7976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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