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- PDB-6wm6: Periplasmic EDTA-binding protein EppA, tetragonal -

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Basic information

Entry
Database: PDB / ID: 6wm6
TitlePeriplasmic EDTA-binding protein EppA, tetragonal
ComponentsExtracellular solute-binding protein, family 5
KeywordsPEPTIDE BINDING PROTEIN / Periplasmic binding protein / EDTA / bioremediation / ABC transporter
Function / homologyPeptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / Extracellular solute-binding protein, family 5
Function and homology information
Biological speciesChelativorans sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsLewis, K.M. / Sattler, S.A. / Greene, C.L. / Xun, L. / Kang, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF CHE-1804699 United States
CitationJournal: Int J Mol Sci / Year: 2020
Title: The Structural Basis of the Binding of Various Aminopolycarboxylates by the Periplasmic EDTA-Binding Protein EppA from Chelativorans sp. BNC1.
Authors: Lewis, K.M. / Greene, C.L. / Sattler, S.A. / Youn, B. / Xun, L. / Kang, C.
History
DepositionApr 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extracellular solute-binding protein, family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,28311
Polymers62,5601
Non-polymers72310
Water10,791599
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.805, 87.805, 164.484
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1022-

HOH

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Components

#1: Protein Extracellular solute-binding protein, family 5


Mass: 62560.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chelativorans sp. (strain BNC1) (bacteria)
Strain: BNC1 / Gene: Meso_1835 / Production host: Escherichia coli (E. coli) / References: UniProt: Q11H97
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.416→41.1 Å / Num. obs: 122095 / % possible obs: 97.4 % / Redundancy: 20 % / Biso Wilson estimate: 20.01 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.57
Reflection shellResolution: 1.416→1.467 Å / Rmerge(I) obs: 0.8602 / Mean I/σ(I) obs: 4.77 / Num. unique obs: 11723 / CC1/2: 0.887

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.2phasing
PHENIX1.15.2_3472refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vr5

1vr5


Resolution: 1.42→41.1 Å / SU ML: 0.1126 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 14.7177
RfactorNum. reflection% reflection
Rfree0.1525 1939 1.63 %
Rwork0.1441 --
obs0.1442 119276 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.13 Å2
Refinement stepCycle: LAST / Resolution: 1.42→41.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4128 0 43 599 4770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734398
X-RAY DIFFRACTIONf_angle_d0.94226008
X-RAY DIFFRACTIONf_chiral_restr0.0781656
X-RAY DIFFRACTIONf_plane_restr0.0075791
X-RAY DIFFRACTIONf_dihedral_angle_d15.99161608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.450.21931170.19577345X-RAY DIFFRACTION86.91
1.45-1.490.20021310.17368022X-RAY DIFFRACTION94.09
1.49-1.530.20231330.16118087X-RAY DIFFRACTION95.17
1.53-1.580.13971290.15548183X-RAY DIFFRACTION95.99
1.58-1.640.17511360.1528177X-RAY DIFFRACTION96.42
1.64-1.710.18471400.14948355X-RAY DIFFRACTION97.79
1.71-1.780.16261400.14798396X-RAY DIFFRACTION98.14
1.78-1.880.18571400.13888440X-RAY DIFFRACTION98.63
1.88-20.14791430.1428526X-RAY DIFFRACTION99.31
2-2.150.15311440.13758591X-RAY DIFFRACTION99.81
2.15-2.370.14711430.13468631X-RAY DIFFRACTION99.92
2.37-2.710.14561450.13698672X-RAY DIFFRACTION99.99
2.71-3.410.13521460.14788767X-RAY DIFFRACTION100
3.41-41.10.15081520.14369145X-RAY DIFFRACTION99.9

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