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- PDB-4reu: Revelation of Endogenously bound Fe2+ ions in the Crystal Structu... -

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Entry
Database: PDB / ID: 4reu
TitleRevelation of Endogenously bound Fe2+ ions in the Crystal Structure of Ferritin from Escherichia coli
ComponentsFerritin
KeywordsOXIDOREDUCTASE / Ferritin / Iron-binding / binuclear metal binding
Function / homologyFerritin, core subunit, four-helix bundle / Ferritin / Up-down Bundle / Mainly Alpha / : / : / :
Function and homology information
Biological speciesEscherichia coli str. K-12 substr. MDS42 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsThiruselvam, V. / Ponnuswamy, M.N. / Kumarevel, T.S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Revelation of endogenously bound Fe(2+) ions in the crystal structure of ferritin from Escherichia coli.
Authors: Thiruselvam, V. / Sivaraman, P. / Kumarevel, T. / Ponnuswamy, M.N.
History
DepositionSep 24, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,94368
Polymers115,8696
Non-polymers4,07362
Water3,549197
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)479,771272
Polymers463,47824
Non-polymers16,293248
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area101900 Å2
ΔGint-2831 kcal/mol
Surface area148400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.998, 127.998, 170.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11D-207-

MG

21E-206-

SO4

31D-303-

HOH

41F-312-

HOH

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Ferritin


Mass: 19311.564 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MDS42 (bacteria)
Gene: ftn, ECMDS42_1565 / Production host: Escherichia coli (E. coli) / References: UniProt: H0QD82, ferroxidase

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Non-polymers , 7 types, 259 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.02 Å3/Da / Density % sol: 59.28 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10mM Mg hexahydrtae, 2.0M Lithium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 23, 2012 / Details: Si III
RadiationMonochromator: Si II / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 45052 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 13.9
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 1.6 / Num. unique all: 4667 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4Molrepmodel building
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALAdata scaling
CCP4Molrepphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EUM

1eum


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.933 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.383 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23539 2402 5.1 %RANDOM
Rwork0.17188 ---
all0.17506 ---
obs0.17506 45052 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.757 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å2-0 Å2
2--0.53 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8148 0 149 197 8494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198422
X-RAY DIFFRACTIONr_bond_other_d0.0050.027627
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9611386
X-RAY DIFFRACTIONr_angle_other_deg0.836317619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6385978
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.21925.526456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.503151506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5641524
X-RAY DIFFRACTIONr_chiral_restr0.0810.21221
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029480
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021992
X-RAY DIFFRACTIONr_mcbond_it3.684.6393930
X-RAY DIFFRACTIONr_mcbond_other3.6754.6383929
X-RAY DIFFRACTIONr_mcangle_it5.766.9364902
X-RAY DIFFRACTIONr_mcangle_other5.7616.9384903
X-RAY DIFFRACTIONr_scbond_it4.2484.8944490
X-RAY DIFFRACTIONr_scbond_other4.2484.8954490
X-RAY DIFFRACTIONr_scangle_other6.5817.1636484
X-RAY DIFFRACTIONr_long_range_B_refined9.79236.19510211
X-RAY DIFFRACTIONr_long_range_B_other9.78936.18310166
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 175 -
Rwork0.249 3314 -
obs--100 %

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