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

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Basic information

Entry
Database: PDB / ID: 6tfq
TitleStructure in P3212 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


ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space
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
alpha-D-glucopyranose / Chem-N72 / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 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: Data collection / Database references / Category: chem_comp / citation
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)114,90934
Polymers111,3622
Non-polymers3,54732
Water14,484804
1
A: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,55118
Polymers55,6811
Non-polymers1,87017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,35816
Polymers55,6811
Non-polymers1,67815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.980, 155.980, 181.750
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

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Components

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Protein / Sugars , 2 types, 4 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: 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: Sugar ChemComp-GLC / alpha-D-glucopyranose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 834 molecules

#3: 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
#4: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 5.84 Å3/Da / Density % sol: 78.93 %
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 EIGER X 16M / 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: 2.05→47.84 Å / Num. obs: 157907 / % possible obs: 99.9 % / Redundancy: 14.36 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.029 / Net I/σ(I): 15.01
Reflection shellResolution: 2.05→2.17 Å / Rmerge(I) obs: 1.613 / Num. unique obs: 25177 / CC1/2: 0.546 / Rpim(I) all: 0.426

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→47.84 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.103 / SU Rfree Blow DPI: 0.097 / SU Rfree Cruickshank DPI: 0.096
RfactorNum. reflection% reflectionSelection details
Rfree0.199 7895 5 %RANDOM
Rwork0.185 ---
obs0.186 157905 99.8 %-
Displacement parametersBiso max: 183.04 Å2 / Biso mean: 54.95 Å2 / Biso min: 34.54 Å2
Baniso -1Baniso -2Baniso -3
1-1.8847 Å20 Å20 Å2
2--1.8847 Å20 Å2
3----3.7694 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 2.05→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7692 0 198 804 8694
Biso mean--103.28 58.6 -
Num. residues----986
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2723SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1361HARMONIC5
X-RAY DIFFRACTIONt_it8047HARMONIC20
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_contact9636SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8047HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10961HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.55
X-RAY DIFFRACTIONt_other_torsion16.69
LS refinement shellResolution: 2.05→2.06 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2743 158 5 %
Rwork0.2505 3001 -
all0.2517 3159 -
obs--91.35 %
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)
10.6545-0.01160.18780.5323-0.14620.5807-0.045-0.0492-0.00560.0860.0145-0.00490.0060.07670.0305-0.16870.0444-0.0251-0.28210.0015-0.217112.0303118.4167-8.2266
20.79590.0036-0.10741.10150.29540.5201-0.0689-0.0870.1060.17960.01470.0218-0.1152-0.06480.0542-0.03270.0756-0.0144-0.219-0.0346-0.1229-14.7608149.1961-9.5858
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|30 - A|367 }A30 - 367
2X-RAY DIFFRACTION2{ B|2 - B|365 }B2 - 365

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