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- PDB-6tfs: Structure in P3212 form of the PBP/SBP MoaA in complex with gluco... -

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Basic information

Entry
Database: PDB / ID: 6tfs
TitleStructure in P3212 form of the PBP/SBP MoaA in complex with glucopinic acid from A.tumefacien R10
ComponentsABC transporter substrate-binding protein
KeywordsTRANSPORT PROTEIN / Solute binding protein / periplasmic binding protein
Function / homology
Function and homology information


peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle
Similarity search - Domain/homology
Chem-N7T / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMorera, S. / Vigouroux, A.
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: ABC transporter substrate-binding protein
B: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,36119
Polymers111,3622
Non-polymers1,99917
Water14,304794
1
A: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,79411
Polymers55,6811
Non-polymers1,11310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5668
Polymers55,6811
Non-polymers8867
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.230, 156.230, 182.640
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein ABC transporter substrate-binding protein / MoaA / Peptide/nickel transport system substrate-binding protein / Polyamine ABC transporter ...MoaA / Peptide/nickel transport system substrate-binding protein / Polyamine ABC transporter substrate-binding protein


Mass: 55680.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: moaA, ddpA, A6U90_18755, At1D1609_52430, AtA6_55190 / Production host: Escherichia coli (E. coli) / References: UniProt: O50271
#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.: 2 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / 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

Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2 M AS, 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 1 / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 2→45 Å / Num. obs: 171659 / % possible obs: 99.5 % / Redundancy: 17.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.035 / Net I/σ(I): 13.61
Reflection shellResolution: 2→2.12 Å / Num. unique obs: 26916 / CC1/2: 0.518 / Rpim(I) all: 0.607

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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: 6TFQ

6tfq


Resolution: 2→29.15 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.095 / SU Rfree Blow DPI: 0.089 / SU Rfree Cruickshank DPI: 0.087
RfactorNum. reflection% reflectionSelection details
Rfree0.194 8580 5 %RANDOM
Rwork0.184 ---
obs0.184 171605 99.5 %-
Displacement parametersBiso max: 152.95 Å2 / Biso mean: 50.99 Å2 / Biso min: 32.88 Å2
Baniso -1Baniso -2Baniso -3
1-3.9316 Å20 Å20 Å2
2--3.9316 Å20 Å2
3----7.8632 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 2→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7692 0 113 794 8599
Biso mean--86.19 57.13 -
Num. residues----986
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2742SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1381HARMONIC5
X-RAY DIFFRACTIONt_it8037HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1053SEMIHARMONIC5
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_contact9670SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8037HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10952HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.49
X-RAY DIFFRACTIONt_other_torsion16.42
LS refinement shellResolution: 2→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3139 172 5.01 %
Rwork0.2911 3261 -
all0.2922 3433 -
obs--79.54 %
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)
10.44450.035-0.04810.5501-0.16990.48820.015-0.04350.00550.0775-0.0498-0.00940.05430.02380.0348-0.2583-0.05720.0015-0.26330.0185-0.2606-47.2238-41.276821.959
21.13440.1890.17340.84470.15820.4430.0372-0.13020.0870.1055-0.0725-0.0581-0.07110.02980.0353-0.2719-0.0817-0.0232-0.2867-0.0169-0.2513-34.1084-2.502120.7456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 494
2X-RAY DIFFRACTION2{ B|* }B2 - 494

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