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- PDB-7kz9: Crystal structure of Pseudomonas sp. PDC86 substrate-binding prot... -

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Basic information

Entry
Database: PDB / ID: 7kz9
TitleCrystal structure of Pseudomonas sp. PDC86 substrate-binding protein Aapf in complex with a signaling molecule HEHEAA
ComponentsPeptide/nickel transport system substrate-binding protein AapF
KeywordsTRANSPORT PROTEIN / substrate-binding protein (SBPs) / ABC-transporter / type-C SBPs
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / 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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / 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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N,N~2~-bis(2-hydroxyethyl)glycinamide / Peptide/nickel transport system substrate-binding protein
Similarity search - Component
Biological speciesPseudomonas sp. PDC86 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLuo, S. / Dadhwal, P. / Tong, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118093 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD012018 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structural basis for a bacterial Pip system plant effector recognition protein.
Authors: Luo, S. / Coutinho, B.G. / Dadhwal, P. / Oda, Y. / Ren, J. / Schaefer, A.L. / Greenberg, E.P. / Harwood, C.S. / Tong, L.
History
DepositionDec 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: Peptide/nickel transport system substrate-binding protein AapF
B: Peptide/nickel transport system substrate-binding protein AapF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,52915
Polymers110,1802
Non-polymers1,34913
Water8,755486
1
A: Peptide/nickel transport system substrate-binding protein AapF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6246
Polymers55,0901
Non-polymers5355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptide/nickel transport system substrate-binding protein AapF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9059
Polymers55,0901
Non-polymers8158
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.395, 62.576, 92.602
Angle α, β, γ (deg.)97.220, 91.650, 89.970
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Peptide/nickel transport system substrate-binding protein AapF


Mass: 55089.922 Da / Num. of mol.: 2 / Fragment: substrate-binding proteins, SBPs
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. PDC86 (bacteria) / Gene: AapF / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: A0A1H3V8R8
#2: Chemical ChemComp-XN7 / N,N~2~-bis(2-hydroxyethyl)glycinamide


Mass: 162.187 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: 0.1 M Bis-Tris (pH 6.5), and 2.6 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→42.38 Å / Num. obs: 71335 / % possible obs: 95.6 % / Redundancy: 2.212 % / Biso Wilson estimate: 36.136 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.104 / Χ2: 1.098 / Net I/σ(I): 7.1 / Num. measured all: 157765
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-2.012.290.7291.122611512089114060.5240.95894.4
2.01-2.152.2630.4241.992464211350108910.7770.55996
2.15-2.322.2030.2693.132223510526100910.9020.35695.9
2.32-2.542.0780.1824.419261969392710.9460.24195.6
2.54-2.842.2270.1236.8618888880284830.9760.16196.4
2.84-3.282.270.07611.0517019778374990.990.09996.4
3.28-4.022.1780.04716.7713523650362080.9940.06195.5
4.02-5.662.0240.04119.559716507448010.9940.05494.6
5.66-42.382.3710.03122.486366281826850.9970.03995.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1uqw

1uqw


Resolution: 1.9→42.38 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 2601 3.65 %
Rwork0.1941 68701 -
obs0.1959 71302 95.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.41 Å2 / Biso mean: 34.4646 Å2 / Biso min: 15.67 Å2
Refinement stepCycle: final / Resolution: 1.9→42.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7546 0 85 486 8117
Biso mean--36.08 34.37 -
Num. residues----955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087768
X-RAY DIFFRACTIONf_angle_d0.93910539
X-RAY DIFFRACTIONf_dihedral_angle_d26.1582873
X-RAY DIFFRACTIONf_chiral_restr0.1611193
X-RAY DIFFRACTIONf_plane_restr0.0051352
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.930.31921320.30353425355790
1.93-1.970.33261430.29073624376796
1.97-2.010.32661380.28383657379596
2.01-2.050.31731310.26153601373296
2.05-2.10.28551400.24843678381896
2.1-2.150.27091330.24163634376796
2.15-2.210.2811340.22493605373996
2.21-2.280.31471350.23083601373696
2.28-2.350.26281330.2243679381296
2.35-2.430.29211400.22863586372695
2.43-2.530.29441310.22523625375696
2.53-2.650.29721370.21673658379596
2.65-2.790.2851440.21263641378596
2.79-2.960.26851370.20273625376297
2.96-3.190.2311430.19753660380396
3.19-3.510.23011360.17983645378196
3.51-4.020.20731450.15953584372995
4.02-5.060.1841310.14783585371695
5.06-42.380.19771380.1553588372695

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