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- PDB-7kz8: Crystal structure of substrate-binding protein Aapf from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 7kz8
TitleCrystal structure of substrate-binding protein Aapf from Pseudomonas sp. PDC86
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 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Peptide/nickel transport system substrate-binding protein
Similarity search - Component
Biological speciesPseudomonas sp. PDC86 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2743
Polymers55,0901
Non-polymers1842
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-0 kcal/mol
Surface area17930 Å2
Unit cell
Length a, b, c (Å)62.252, 41.961, 93.143
Angle α, β, γ (deg.)90.000, 99.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 55089.922 Da / Num. of mol.: 1 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.18 Å3/Da / Density % sol: 43.52 %
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 / Details: Dectris Eiger 9M
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→47.53 Å / Num. obs: 23962 / % possible obs: 98.1 % / Redundancy: 4.049 % / Biso Wilson estimate: 41.78 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.173 / Χ2: 0.966 / Net I/σ(I): 6.93 / Num. measured all: 97033
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
2.2-2.344.030.8821.4515021390137270.7071.02295.5
2.34-2.53.8170.6691.9613830368736230.8240.78298.3
2.5-2.73.9830.5072.8713418340433690.8920.58899
2.7-2.954.2850.3674.5613413315431300.9260.42199.2
2.95-3.34.2620.1977.7112126287628450.9720.22698.9
3.3-3.814.1040.10811.7110285255125060.9840.12598.2
3.81-4.663.7460.08214.847963217321260.9870.09697.8
4.66-6.554.1170.07316.276806167916530.9890.08598.5
6.55-47.534.2430.04720.23417110039830.9940.05498

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1uqw

1uqw


Resolution: 2.2→47.53 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 29.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 1195 4.99 %
Rwork0.2178 22733 -
obs0.2202 23928 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.82 Å2 / Biso mean: 40.4541 Å2 / Biso min: 18.07 Å2
Refinement stepCycle: final / Resolution: 2.2→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3772 0 12 141 3925
Biso mean--36.18 36.48 -
Num. residues----477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173857
X-RAY DIFFRACTIONf_angle_d1.2935239
X-RAY DIFFRACTIONf_dihedral_angle_d24.8981427
X-RAY DIFFRACTIONf_chiral_restr0.099596
X-RAY DIFFRACTIONf_plane_restr0.007675
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.290.33911260.30762386251294
2.29-2.40.35411330.29492518265198
2.4-2.520.35041330.29912503263698
2.52-2.680.3251290.29062526265599
2.68-2.890.31131360.26852530266699
2.89-3.180.32591300.22992563269399
3.18-3.640.26181310.20662518264998
3.64-4.580.22381390.17322550268998
4.58-47.530.2041380.17382639277798

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