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- PDB-5y4c: Crystal structure of EfeO-like protein Algp7 in complex with a me... -

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Basic information

Entry
Database: PDB / ID: 5y4c
TitleCrystal structure of EfeO-like protein Algp7 in complex with a metal ion
ComponentsAlginate-binding protein
KeywordsSTRUCTURAL PROTEIN / two up-and-down four-helical bundles / alginate binding / metal binding
Function / homology
Function and homology information


cell envelope / metal ion binding
Similarity search - Function
EfeO/Algp7, imelysin-like domain / : / : / M75 peptidase, HXXE motif / Imelysin-like domain / Imelysin-like domain superfamily / Imelysin / A middle domain of Talin 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / Alginate-binding protein
Similarity search - Component
Biological speciesSphingomonas sp. A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsTemtrirath, K. / Maruyama, Y. / Mikami, B. / Murata, K. / Hashimoto, W.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Binding mode of metal ions to the bacterial iron import protein EfeO
Authors: Temtrirath, K. / Okumura, K. / Maruyama, Y. / Mikami, B. / Murata, K. / Hashimoto, W.
History
DepositionAug 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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: Alginate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8573
Polymers31,7011
Non-polymers1562
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-11 kcal/mol
Surface area11180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.626, 56.638, 71.173
Angle α, β, γ (deg.)90.00, 122.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alginate-binding protein / EfeO-like protein


Mass: 31701.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. A1 (bacteria) / Gene: p7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q25C86
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% polyethylene glycol 1500, 0.1M sodium 4-(2-hydroxyethyl)-1-piperazineethanesulfonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 7437 / % possible obs: 98.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 21.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.33 / Num. unique all: 690 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AT7

3at7


Resolution: 2.701→30.551 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2757 342 4.62 %
Rwork0.203 --
obs0.2064 7409 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.701→30.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 7 5 1972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061999
X-RAY DIFFRACTIONf_angle_d0.9712692
X-RAY DIFFRACTIONf_dihedral_angle_d14.364750
X-RAY DIFFRACTIONf_chiral_restr0.035299
X-RAY DIFFRACTIONf_plane_restr0.004351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.701-3.40230.31771810.23413439X-RAY DIFFRACTION97
3.4023-30.55240.25641610.19153628X-RAY DIFFRACTION99

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