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- PDB-1qgh: THE X-RAY STRUCTURE OF THE UNUSUAL DODECAMERIC FERRITIN FROM LIST... -

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Basic information

Entry
Database: PDB / ID: 1qgh
TitleTHE X-RAY STRUCTURE OF THE UNUSUAL DODECAMERIC FERRITIN FROM LISTERIA INNOCUA, REVEALS A NOVEL INTERSUBUNIT IRON BINDING SITE.
ComponentsNON-HEME IRON-CONTAINING FERRITIN
KeywordsMETAL TRANSPORT / FERRITIN
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA protection during starvation protein
Similarity search - Component
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsIlari, A. / Stefanini, S. / Chiancone, E. / Tsernoglou, D.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site.
Authors: Ilari, A. / Stefanini, S. / Chiancone, E. / Tsernoglou, D.
History
DepositionApr 27, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jan 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NON-HEME IRON-CONTAINING FERRITIN
B: NON-HEME IRON-CONTAINING FERRITIN
C: NON-HEME IRON-CONTAINING FERRITIN
D: NON-HEME IRON-CONTAINING FERRITIN
E: NON-HEME IRON-CONTAINING FERRITIN
F: NON-HEME IRON-CONTAINING FERRITIN
G: NON-HEME IRON-CONTAINING FERRITIN
H: NON-HEME IRON-CONTAINING FERRITIN
I: NON-HEME IRON-CONTAINING FERRITIN
J: NON-HEME IRON-CONTAINING FERRITIN
K: NON-HEME IRON-CONTAINING FERRITIN
L: NON-HEME IRON-CONTAINING FERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,51724
Polymers216,84712
Non-polymers67012
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38490 Å2
ΔGint-369 kcal/mol
Surface area60820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.540, 137.500, 173.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.02534, -0.00322, -0.99967), (-0.00289, -0.99999, 0.00315), (-0.99967, 0.00281, -0.0253)30.92601, 0.14676, 31.67621
2given(-0.56524, -0.69426, 0.44554), (-0.69392, 0.10811, -0.71189), (0.44607, -0.71156, -0.54287)16.93955, 22.19773, 17.90978
3given(-0.45944, 0.69427, 0.55399), (0.69698, -0.10482, 0.70939), (0.55058, 0.71204, -0.43573)13.46489, -21.91316, 14.38429
4given(-0.20491, 0.21849, -0.95408), (0.86458, 0.49734, -0.0718), (0.45882, -0.83959, -0.29081)33.73081, -11.88506, 13.68209
5given(0.94931, -0.21652, 0.22787), (0.09265, -0.49997, -0.86107), (0.30037, 0.83854, -0.45457)-2.64692, 12.34241, 18.55365
6given(-0.46544, 0.84452, 0.26487), (-0.86353, -0.49893, 0.07336), (0.1941, -0.19458, 0.96149)18.20738, 12.1298, -2.29897
7given(-0.27795, -0.84229, 0.46184), (-0.09476, 0.50248, 0.85938), (-0.95591, 0.1951, -0.21948)12.36059, -12.03838, 33.96724
8given(-0.20941, 0.86728, 0.45163), (0.21646, 0.49152, -0.84353), (-0.95357, -0.07889, -0.29066)11.43735, 10.10695, 34.9837
9given(-0.4642, -0.86409, 0.19457), (0.84394, -0.49818, -0.19896), (0.26886, 0.07185, 0.9605)19.50842, -9.60517, -3.5069
10given(-0.28023, -0.09486, -0.95523), (-0.84316, 0.49999, 0.1977), (0.45885, 0.86082, -0.2201)34.7996, 9.82864, 12.27548
11given(0.94789, 0.09683, 0.30353), (-0.21849, -0.49583, 0.84048), (0.23189, -0.863, -0.44883)-3.86911, -9.90294, 19.56981

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Components

#1: Protein
NON-HEME IRON-CONTAINING FERRITIN


Mass: 18070.553 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / References: UniProt: P80725
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growpH: 5.8
Details: PEG 1000 AT 19-25 %, MES 0.1 M AT PH 5.0-6.2, pH 5.8
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
20.1 MMES1reservoir
319-25 %PEG10001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8373
DetectorDate: Dec 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8373 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 80150 / % possible obs: 91.3 % / Redundancy: 3.8 % / Rsym value: 0.077
Reflection
*PLUS
Rmerge(I) obs: 0.077

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DPS

1dps


Resolution: 2.35→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.219 --
all0.219 --
obs-80098 91 %
Refinement stepCycle: LAST / Resolution: 2.35→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14664 0 12 479 15155
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.039
X-RAY DIFFRACTIONt_dihedral_angle_d14.698
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.011
X-RAY DIFFRACTIONt_gen_planes0.016
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg14.698
X-RAY DIFFRACTIONt_plane_restr0.016

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