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- PDB-1gwg: Tri-iodide derivative of apoferritin -

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Basic information

Entry
Database: PDB / ID: 1gwg
TitleTri-iodide derivative of apoferritin
ComponentsFERRITIN LIGHT CHAIN
KeywordsFERRITIN / IRON STORAGE / MULTIGENE FAMILY / ACETYLATION
Function / homology
Function and homology information


ferritin complex / autolysosome / intracellular sequestering of iron ion / autophagosome / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasmic vesicle / iron ion binding / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / 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 iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / 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
: / IODIDE ION / Ferritin light chain
Similarity search - Component
Biological speciesEQUUS CABALLUS (horse)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.01 Å
AuthorsEvans, G. / Bricogne, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Triiodide Derivatization and Combinatorial Counter-Ion Replacement: Two Methods for Enhancing Phasing Signal Using Laboratory Cu Kalpha X-Ray Equipment
Authors: Evans, G. / Bricogne, G.
History
DepositionMar 15, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERRITIN LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,23912
Polymers19,8721
Non-polymers1,36711
Water2,738152
1
A: FERRITIN LIGHT CHAIN
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)509,745288
Polymers476,93824
Non-polymers32,807264
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation24_555-z,-y,-x1
crystal symmetry operation14_555-y,-x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)181.190, 181.190, 181.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-1178-

CD

21A-1179-

CD

31A-1181-

IOD

41A-2040-

HOH

51A-2125-

HOH

61A-2126-

HOH

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Components

#1: Protein FERRITIN LIGHT CHAIN / FERRITIN L SUBUNIT / FERRITIN


Mass: 19872.428 Da / Num. of mol.: 1 / Fragment: L-CHAIN RESIDUES 1-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EQUUS CABALLUS (horse) / Organ: SPLEEN / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02791
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.31 Å3/Da / Density % sol: 62 %
Crystal growpH: 5.3
Details: 40MG/ML PROTEIN; 8MM CDSO4, 1M AMMONIUM SULPHATE, 0.01M NAN3., pH 5.30
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-40 mg/mlprotein1drop
20.1 M1dropNaCl
37-12 mM1reservoirCdSO4
41 Mammonium sulfate1reservoir
53 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Aug 15, 2000 / Details: SUPPER MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→22.14 Å / Num. obs: 406056 / % possible obs: 98.8 % / Observed criterion σ(I): 6 / Redundancy: 9.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.1
Reflection shellResolution: 2.01→2.12 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.4 / % possible all: 98.8
Reflection
*PLUS
% possible obs: 98.9 %
Reflection shell
*PLUS
% possible obs: 93 % / Redundancy: 6.2 %

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Processing

Software
NameClassification
BUSTER-TNTrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.01→22.14 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.208 872 5 %RANDOM
Rwork0.167 ---
obs0.169 17264 99.8 %-
Refinement stepCycle: LAST / Resolution: 2.01→22.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 11 152 1517
Refinement
*PLUS
Num. reflection obs: 17272 / Rfactor obs: 0.169 / Rfactor Rfree: 0.205 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg1.283

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