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- PDB-6hm2: Structure in P1 form of the PBP AgtB in complex with agropinic ac... -

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Basic information

Entry
Database: PDB / ID: 6hm2
TitleStructure in P1 form of the PBP AgtB in complex with agropinic acid from A.tumefacien R10
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 / :
Function and homology information
Biological speciesAgrobacterium tumefaciens LBA4213
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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 12, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Agropine permease
B: Agropine permease
C: Agropine permease
D: Agropine permease
E: Agropine permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,56623
Polymers186,4595
Non-polymers2,10718
Water18,3571019
1
A: Agropine permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7305
Polymers37,2921
Non-polymers4384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Agropine permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7305
Polymers37,2921
Non-polymers4384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Agropine permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7305
Polymers37,2921
Non-polymers4384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Agropine permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7926
Polymers37,2921
Non-polymers5005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Agropine permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5832
Polymers37,2921
Non-polymers2911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.570, 86.310, 106.520
Angle α, β, γ (deg.)71.14, 81.00, 76.32
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Agropine permease


Mass: 37291.898 Da / Num. of mol.: 5
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
#2: Chemical
ChemComp-G9Z / agropinic acid


Mass: 291.255 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C11H17NO8
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1019 / 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 % sol: 32.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 8K, 0.1 M Tris, 0.2 M CaCl2

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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: 1.74→50 Å / Num. obs: 129664 / % possible obs: 95.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 24.08 Å2 / Rsym value: 0.119 / Net I/σ(I): 7.58
Reflection shellResolution: 1.74→1.85 Å / Rsym value: 0.897

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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: 1.74→49.73 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.127 / SU Rfree Blow DPI: 0.112 / SU Rfree Cruickshank DPI: 0.113
RfactorNum. reflection% reflectionSelection details
Rfree0.201 6483 5 %RANDOM
Rwork0.174 ---
obs0.175 129660 95.9 %-
Displacement parametersBiso mean: 36.62 Å2
Baniso -1Baniso -2Baniso -3
1-3.6952 Å2-1.3358 Å2-0.2852 Å2
2--2.3886 Å20.617 Å2
3----6.0838 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: 1 / Resolution: 1.74→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12075 0 140 1019 13234
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112509HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9817021HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4110SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2106HARMONIC5
X-RAY DIFFRACTIONt_it12509HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.4
X-RAY DIFFRACTIONt_other_torsion16.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1613SEMIHARMONIC5
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_contact15895SEMIHARMONIC4
LS refinement shellResolution: 1.74→1.76 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.27 129 4.97 %
Rwork0.2744 2465 -
all0.2742 2594 -
obs--62.62 %
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)
10.61810.20150.13951.11190.39360.4555-0.0231-0.06360.01570.02490.0217-0.04940.0142-0.00680.0015-0.11270.0111-0.0052-0.12320.0063-0.106219.7316-26.30718.0366
20.5808-0.2346-0.11710.89960.23180.342-0.01630.0554-0.0269-0.03260.0186-0.0161-0.0247-0.0168-0.0023-0.1172-0.0019-0.0087-0.1170-0.099640.0436-59.9664-17.0316
30.47030.09630.03390.30480.11441.2410.027-0.0753-0.03340.05210.0068-0.0251-0.0060.0261-0.0338-0.10470.0123-0.0142-0.12530.0139-0.11312.3353-68.381523.3027
40.4145-0.1305-0.03520.46310.24731.01020.03870.05630.0171-0.04340.0112-0.026-0.00060.0143-0.0499-0.10810.0043-0.0022-0.12330.0117-0.110832.4164-18.0726-22.3201
53.85770.40043.75663.5089-1.79968.8926-0.09840.77990.2348-0.36090.28490.18930.53180.3914-0.18650.1432-0.0844-0.0550.15160.0658-0.203117.2209-54.6602-46.1018
60.19230.0628-0.09320.534-0.07870.14490.00520.0595-0.0007-0.08920.0301-0.02310.0147-0.0145-0.0353-0.10640.0015-0.0530.0137-0.0167-0.034324.8461-46.8609-8.6661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }

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