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- PDB-6tg2: Structure of the PBP/SBP MotA in complex with mannopinic acid fro... -

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Basic information

Entry
Database: PDB / ID: 6tg2
TitleStructure of the PBP/SBP MotA in complex with mannopinic acid from A.tumefacien R10
ComponentsMotA
KeywordsTRANSPORT PROTEIN / Solute binding protein / periplasmic binding protein
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / metal ion binding / Chem-N72 / DI(HYDROXYETHYL)ETHER / MotA
Function and homology information
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsMorera, S. / Marty, L.
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 ...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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MotA
B: MotA
C: MotA
D: MotA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,74020
Polymers153,8244
Non-polymers1,91616
Water4,846269
1
A: MotA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0728
Polymers38,4561
Non-polymers6167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MotA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8674
Polymers38,4561
Non-polymers4113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MotA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9955
Polymers38,4561
Non-polymers5404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MotA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8053
Polymers38,4561
Non-polymers3492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.920, 132.130, 69.460
Angle α, β, γ (deg.)90.000, 91.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
MotA


Mass: 38455.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: motA, A6U90_18895 / Production host: Escherichia coli (E. coli) / References: UniProt: Q44384

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Non-polymers , 5 types, 285 molecules

#2: Chemical
ChemComp-N72 / (2~{R})-2-[[(3~{R},4~{R},5~{S})-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.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.03 Å3/Da / Density % sol: 39.28 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 4K, 100 mM Tris HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→45 Å / Num. obs: 60300 / % possible obs: 97.8 % / Redundancy: 3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.093 / Net I/σ(I): 6.31
Reflection shellResolution: 2.2→2.34 Å / Rmerge(I) obs: 0.907 / Num. unique obs: 9388 / CC1/2: 0.51

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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: 2.21→31.19 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.291 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.201
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3014 5 %RANDOM
Rwork0.185 ---
obs0.187 60285 97.8 %-
Displacement parametersBiso max: 145.94 Å2 / Biso mean: 43.21 Å2 / Biso min: 17.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.6837 Å20 Å23.9017 Å2
2--5.6317 Å20 Å2
3----7.3154 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 2.21→31.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10000 0 120 269 10389
Biso mean--41.81 41.4 -
Num. residues----1300
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3439SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1770HARMONIC5
X-RAY DIFFRACTIONt_it10356HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1355SEMIHARMONIC5
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_contact12114SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10356HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg14063HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion18.95
LS refinement shellResolution: 2.21→2.22 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3444 60 4.98 %
Rwork0.2747 1146 -
all0.2782 1206 -
obs--75.02 %
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)
11.25310.22060.04641.5155-0.1380.7791-0.038-0.0280.1475-0.00490.05720.0029-0.044-0.013-0.0193-0.08750.0111-0.0132-0.0445-0.0241-0.091119.87380.4446-47.5987
21.2293-0.36330.27212.3392-0.04780.68260.09940.0172-0.1292-0.0972-0.12350.08870.0620.0470.0241-0.10350.01490.0088-0.0631-0.0021-0.1247.131-21.4685-43.1716
30.64120.17310.03823.0008-0.58181.27520.01710.0642-0.044-0.16330.0147-0.02360.1520.0026-0.0318-0.05510.0299-0.0082-0.0644-0.0044-0.1626-9.582910.6108-81.3535
40.7953-0.23090.19842.12520.34511.0356-0.0255-0.00340.0716-0.1264-0.03830.0493-0.1736-0.0060.0638-0.0403-0.01590.001-0.06980.0183-0.1629-9.586533.0486-54.3127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|29 - A|354 }A29 - 354
2X-RAY DIFFRACTION2{ B|30 - B|353 }B30 - 353
3X-RAY DIFFRACTION3{ C|31 - C|356 }C31 - 356
4X-RAY DIFFRACTION4{ D|30 - D|352 }D30 - 352

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