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- PDB-6tfx: Structure in P21 form of the PBP/SBP MoaA in complex with mannopi... -

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Basic information

Entry
Database: PDB / ID: 6tfx
TitleStructure in P21 form of the PBP/SBP MoaA in complex with mannopinic 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 transport / peptide transmembrane transporter activity / 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-N72 / DI(HYDROXYETHYL)ETHER / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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

Downloads & links

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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)111,90112
Polymers110,8932
Non-polymers1,00810
Water14,808822
1
A: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9726
Polymers55,4461
Non-polymers5265
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9286
Polymers55,4461
Non-polymers4825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.050, 77.930, 104.040
Angle α, β, γ (deg.)90.000, 107.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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: 55446.348 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

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Non-polymers , 5 types, 832 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.: 2 / 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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 4K, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→47.56 Å / Num. obs: 134434 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.04 / Net I/σ(I): 9.4
Reflection shellResolution: 1.56→1.66 Å / Rmerge(I) obs: 0.947 / Num. unique obs: 21895 / CC1/2: 0.646

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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: 1.56→47.56 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.076 / SU Rfree Blow DPI: 0.073 / SU Rfree Cruickshank DPI: 0.072
RfactorNum. reflection% reflectionSelection details
Rfree0.182 6722 5 %RANDOM
Rwork0.163 ---
obs0.164 134431 99.4 %-
Displacement parametersBiso max: 110.6 Å2 / Biso mean: 24.56 Å2 / Biso min: 10.68 Å2
Baniso -1Baniso -2Baniso -3
1--2.1476 Å20 Å21.2109 Å2
2--2.2698 Å20 Å2
3----0.1222 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: final / Resolution: 1.56→47.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7702 0 65 822 8589
Biso mean--27.63 32.11 -
Num. residues----987
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2762SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1387HARMONIC5
X-RAY DIFFRACTIONt_it8033HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1058SEMIHARMONIC5
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_contact9945SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8033HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10937HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.88
X-RAY DIFFRACTIONt_other_torsion15.08
LS refinement shellResolution: 1.56→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.4301 135 5.02 %
Rwork0.3774 2554 -
all0.3801 2689 -
obs--79.8 %
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)
10.3258-0.06870.16980.3436-0.08420.29450.0110.0390.00620.0062-0.006-0.0462-0.02410.0621-0.005-0.06430.00080.0148-0.0708-0.0131-0.057745.240992.0871126.0622
20.4155-0.1242-0.15050.32820.15940.3543-0.00060.0207-0.04870.0016-0.03670.07620.018-0.05690.0372-0.07770.00380.015-0.08040.005-0.042318.573357.9609125.4926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A30 - 522
2X-RAY DIFFRACTION2{ B|* }B30 - 523

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