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- PDB-6tg3: Crystal Structure of the PBP/SBP MotA in complex with glucopinic ... -

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Basic information

Entry
Database: PDB / ID: 6tg3
TitleCrystal Structure of the PBP/SBP MotA in complex with glucopinic acid from A. tumefaciens B6/R10
ComponentsMotA
KeywordsTRANSPORT PROTEIN / solute binding protein / periplasmic binding protein
Function / homology
Function and homology information


thiamine binding / thiamine transport / thiamine pyrophosphate binding / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Biological speciesRhizobium radiobacter (Agrobacterium genomosp. 4)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMorera, S. / Vigouroux, S.
CitationJournal: Biochem.J. / Year: 2020
Title: Import pathways of the mannityl-opines into the bacterial pathogen Agrobacterium tumefaciens: structural, affinity and in vivo approaches.
Authors: Vigouroux, A. / Dore, J. / Marty, L. / Aumont-Nicaise, M. / Legrand, P. / Dessaux, Y. / Vial, L. / Morera, S.
History
DepositionNov 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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: MotA
B: MotA
C: MotA
D: MotA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,18510
Polymers153,8244
Non-polymers1,3616
Water6,143341
1
A: MotA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8273
Polymers38,4561
Non-polymers3712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MotA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7652
Polymers38,4561
Non-polymers3091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MotA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7652
Polymers38,4561
Non-polymers3091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MotA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8273
Polymers38,4561
Non-polymers3712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.630, 131.930, 70.380
Angle α, β, γ (deg.)90.000, 91.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MotA


Mass: 38455.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (Agrobacterium genomosp. 4)
Gene: motA, A6U90_18895 / Production host: Escherichia coli (E. coli) / References: UniProt: Q44384
#2: Chemical
ChemComp-N7T / (2~{S})-2-[[(3~{S},4~{R},5~{R})-3,4,5,6-tetrakis(oxidanyl)-2-oxidanylidene-hexyl]amino]pentanedioic acid


Mass: 309.270 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 4K, 100 mM Tris HCl, 200 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.85→48.12 Å / Num. obs: 106626 / % possible obs: 99.5 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.034 / Net I/σ(I): 12.42
Reflection shellResolution: 1.85→1.96 Å / Rmerge(I) obs: 1.143 / Num. unique obs: 16773 / CC1/2: 0.699 / Rpim(I) all: 0.462

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L9G

5l9g


Resolution: 1.85→48.12 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.129 / SU Rfree Blow DPI: 0.112 / SU Rfree Cruickshank DPI: 0.115
RfactorNum. reflection% reflectionSelection details
Rfree0.199 5332 5 %RANDOM
Rwork0.179 ---
obs0.18 106623 99.5 %-
Displacement parametersBiso max: 148.3 Å2 / Biso mean: 45.39 Å2 / Biso min: 16.63 Å2
Baniso -1Baniso -2Baniso -3
1--5.2824 Å20 Å22.7168 Å2
2--8.2602 Å20 Å2
3----2.9778 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.85→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10008 0 92 341 10441
Biso mean--38.55 41.11 -
Num. residues----1302
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3439SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1774HARMONIC5
X-RAY DIFFRACTIONt_it10354HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1357SEMIHARMONIC5
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_contact12117SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10354HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg14073HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion18.1
LS refinement shellResolution: 1.85→1.86 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.349 107 5.02 %
Rwork0.2965 2026 -
all0.2991 2133 -
obs--81.47 %
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)
10.8242-0.43270.30613.85750.22151.1618-0.1202-0.01530.03780.1336-0.03590.0311-0.1963-0.00380.156-0.0561-0.0202-0.0392-0.1379-0.0048-0.1909-45.7207-0.605315.3574
21.11540.66240.23593.52880.1450.6889-0.0458-0.06490.2246-0.08870.02850.1203-0.041-0.0570.0173-0.14540.0292-0.0349-0.1121-0.0223-0.1232-15.9958-33.112422.2972
30.86350.4589-0.0795.3354-0.50551.4416-0.0440.0715-0.1506-0.03580.0235-0.30630.2709-0.00240.0205-0.07830.0228-0.0214-0.1662-0.0305-0.1944-45.3369-23.0889-11.7636
41.66241.25340.28645.99850.28110.66040.13310.05680.00760.1355-0.09430.08640.0958-0.0435-0.0387-0.1814-0.0170.0262-0.1655-0.0195-0.1449-13.448211.000243.9504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A28 - 353
2X-RAY DIFFRACTION2{ B|* }B29 - 354
3X-RAY DIFFRACTION3{ C|* }C31 - 353
4X-RAY DIFFRACTION4{ D|* }D28 - 354

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