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- PDB-4ynx: Structure of YdiE from E. coli -

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Basic information

Entry
Database: PDB / ID: 4ynx
TitleStructure of YdiE from E. coli
ComponentsUncharacterized protein YdiE
KeywordsUNKNOWN FUNCTION / heme uptake / small / homo-dimer / conserved
Function / homologyHemin uptake protein HemP / Hemin uptake protein hemP / Complement Module, domain 1 / Complement Module; domain 1 / Ribbon / protein homodimerization activity / Mainly Beta / Uncharacterized protein YdiE
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTame, J.R.H. / Nishimura, K. / Zhang, K.Y.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: The crystal and solution structure of YdiE from Escherichia coli
Authors: Nishimura, K. / Addy, C. / Shrestha, R. / Voet, A.R. / Zhang, K.Y.J. / Ito, Y. / Tame, J.R.H.
History
DepositionMar 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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: Uncharacterized protein YdiE
B: Uncharacterized protein YdiE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0174
Polymers14,8252
Non-polymers1922
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-34 kcal/mol
Surface area5900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.736, 38.189, 54.728
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein YdiE


Mass: 7412.448 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ydiE / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0ACX9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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

CrystalDescription: Crystallization was carried out with full-length YdiE protein, but over 20 residues of each chain are missing from the final electron density map. The Matthews coefficient for the ...Description: Crystallization was carried out with full-length YdiE protein, but over 20 residues of each chain are missing from the final electron density map. The Matthews coefficient for the structure is 1.3, assuming all residues to be present, implying a solvent content of under 10%. If only the ordered residues are present in the crystal, the Matthews coefficient is 2.0, implying a solvent content of 40%. NMR experiments confirm the full-length protein was expressed and purified, but a number of residues are apparently missing from the N-terminus of the crystallized protein.
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 1.6 M ammonium sulphate, 0.1M Tris

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.497→30.5 Å / Num. obs: 12710 / % possible obs: 98.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.063 / Net I/av σ(I): 28.4 / Net I/σ(I): 19.3
Reflection shellResolution: 1.497→1.554 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 4.1 / % possible all: 95.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MOLECULAR DYNAMICS SIMULATION OF PDB 2JRA

2jra


Resolution: 1.5→30.5 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.241 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 623 4.9 %RANDOM
Rwork0.1712 ---
obs0.175 12085 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 75.67 Å2 / Biso mean: 16.45 Å2 / Biso min: 5.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2--0.05 Å2-0 Å2
3---0.71 Å2
Refinement stepCycle: final / Resolution: 1.5→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms648 0 10 45 703
Biso mean--26.04 27.82 -
Num. residues----82
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022667
X-RAY DIFFRACTIONr_angle_refined_deg2.0282.044897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.436582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30923.625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05215137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.59156
X-RAY DIFFRACTIONr_chiral_restr0.1390.2105
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021462
X-RAY DIFFRACTIONr_mcbond_it2.4881.5410
X-RAY DIFFRACTIONr_mcangle_it3.8142661
X-RAY DIFFRACTIONr_scbond_it5.6933257
X-RAY DIFFRACTIONr_scangle_it8.6664.5235
X-RAY DIFFRACTIONr_rigid_bond_restr2.6643667
LS refinement shellResolution: 1.498→1.536 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 53 -
Rwork0.215 826 -
all-879 -
obs--100 %

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