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- PDB-5l9g: Crystal Structure of the PBP MotA in complex with mannopine from ... -

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Basic information

Entry
Database: PDB / ID: 5l9g
TitleCrystal Structure of the PBP MotA in complex with mannopine from A. tumefaciens B6
Componentsperiplasmic binding protein
KeywordsTRANSPORT PROTEIN / periplasmic binding protein ABC transporter
Function / homologymannopine / :
Function and homology information
Biological speciesAgrobacterium tumefaciens str. B6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMarty, L. / Morera, S.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BSV8-0003-01 France
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 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: periplasmic binding protein
B: periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,43820
Polymers76,9122
Non-polymers1,52618
Water7,134396
1
A: periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,21910
Polymers38,4561
Non-polymers7639
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,21910
Polymers38,4561
Non-polymers7639
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.220, 71.220, 135.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein periplasmic binding protein


Mass: 38455.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. B6 (bacteria)
Gene: ASB65_13110 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: A0A109C781
#2: Chemical ChemComp-MO0 / mannopine


Mass: 310.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H22N2O8
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% Peg 4K, 0.2 M CaCl2, 50 mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 67490 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 39.35 Å2 / Rsym value: 0.083 / Net I/σ(I): 9.43
Reflection shellResolution: 1.75→1.96 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EUO

4euo


Resolution: 1.75→49 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.108 / SU Rfree Blow DPI: 0.104 / SU Rfree Cruickshank DPI: 0.104
RfactorNum. reflection% reflectionSelection details
Rfree0.208 3374 5 %RANDOM
Rwork0.177 ---
obs0.178 67470 99.9 %-
Displacement parametersBiso mean: 47.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.9114 Å20 Å20 Å2
2---0.9114 Å20 Å2
3---1.8229 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.75→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4991 0 94 413 5498
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015192HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.967033HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1725SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes140HARMONIC2
X-RAY DIFFRACTIONt_gen_planes741HARMONIC5
X-RAY DIFFRACTIONt_it5192HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion669SEMIHARMONIC5
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_contact6326SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 248 5.01 %
Rwork0.257 4703 -
all0.257 4951 -
obs--99.53 %
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)
13.09370.396-0.13740.8332-0.18721.77740.314-0.73230.46510.0682-0.180.06290.00470.1039-0.1341-0.2839-0.08270.057-0.085-0.1508-0.176186.47123.07050.7469
20.6705-0.04480.0811.6103-0.03432.54150.04220.0485-0.0582-0.15440.14850.20010.1842-0.0981-0.1907-0.185-0.0196-0.0578-0.22190.0429-0.1193117.806-12.443312.6302
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|30 - A|354 }
2X-RAY DIFFRACTION2{ B|30 - B|352 }

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