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- PDB-1eum: CRYSTAL STRUCTURE OF THE E.COLI FERRITIN ECFTNA -

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Basic information

Entry
Database: PDB / ID: 1eum
TitleCRYSTAL STRUCTURE OF THE E.COLI FERRITIN ECFTNA
ComponentsFERRITIN 1
KeywordsMETAL BINDING PROTEIN / E.coli non heme Ferritin / EcFtnA
Function / homology
Function and homology information


bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / cellular response to iron ion / ferrous iron binding / iron ion transport / response to oxidative stress / DNA damage response / identical protein binding ...bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / cellular response to iron ion / ferrous iron binding / iron ion transport / response to oxidative stress / DNA damage response / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bacterial non-heme ferritin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.05 Å
AuthorsStillman, T.J. / Hempstead, P.D. / Artymiuk, P.J. / Andrews, S.C. / Hudson, A.J. / Treffry, A. / Guest, J.R. / Harrison, P.M.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The high-resolution X-ray crystallographic structure of the ferritin (EcFtnA) of Escherichia coli; comparison with human H ferritin (HuHF) and the structures of the Fe(3+) and Zn(2+) derivatives.
Authors: Stillman, T.J. / Hempstead, P.D. / Artymiuk, P.J. / Andrews, S.C. / Hudson, A.J. / Treffry, A. / Guest, J.R. / Harrison, P.M.
History
DepositionApr 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERRITIN 1
B: FERRITIN 1
C: FERRITIN 1
D: FERRITIN 1
E: FERRITIN 1
F: FERRITIN 1


Theoretical massNumber of molelcules
Total (without water)116,6576
Polymers116,6576
Non-polymers00
Water7,080393
1
A: FERRITIN 1
B: FERRITIN 1
C: FERRITIN 1
D: FERRITIN 1
E: FERRITIN 1
F: FERRITIN 1

A: FERRITIN 1
B: FERRITIN 1
C: FERRITIN 1
D: FERRITIN 1
E: FERRITIN 1
F: FERRITIN 1

A: FERRITIN 1
B: FERRITIN 1
C: FERRITIN 1
D: FERRITIN 1
E: FERRITIN 1
F: FERRITIN 1

A: FERRITIN 1
B: FERRITIN 1
C: FERRITIN 1
D: FERRITIN 1
E: FERRITIN 1
F: FERRITIN 1


Theoretical massNumber of molelcules
Total (without water)466,62624
Polymers466,62624
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area68930 Å2
ΔGint-511 kcal/mol
Surface area141520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)129.920, 129.920, 173.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
DetailsThe biological assembly is a 24-mer with 432 symmetry. The tetracosamer is generated from the six subunits in the asymmetric unit by the four-fold

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Components

#1: Protein
FERRITIN 1


Mass: 19442.762 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PUC18A2 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A998
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 3.13 Å3/Da / Density % sol: 60.74 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 5.2
Details: 20 mM Piperazine HCl Buffer, 1mM EDTA, 0.1 - 0.6M NaCl, pH 5.2, MICRODIALYSIS, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMpiperazine/HCl11
21 mMEDTA11
30.1-0.6 M11NaCl

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 12, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→39.2 Å / Num. all: 202488 / Num. obs: 87413 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 32.05 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 8.6
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.43 / Num. unique all: 6615 / % possible all: 100
Reflection
*PLUS
Num. measured all: 202488
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
TNTrefinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TNTphasing
RefinementResolution: 2.05→39.2 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.247 4422 -RANDOM
Rwork0.186 ---
all0.188 87405 --
obs0.188 82983 90 %-
Refinement stepCycle: LAST / Resolution: 2.05→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8004 0 0 393 8397
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.007
X-RAY DIFFRACTIONt_angle_deg0.629

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