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- PDB-2v2j: Wild type recombinant horse spleen apoferritin cocrystallized wit... -

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Basic information

Entry
Database: PDB / ID: 2v2j
TitleWild type recombinant horse spleen apoferritin cocrystallized with haemin in basic conditions
ComponentsFERRITIN LIGHT CHAIN
KeywordsMETAL TRANSPORT / IRON / IRON STORAGE / METAL-BINDING
Function / homology
Function and homology information


ferritin complex / autolysosome / ferric iron binding / autophagosome / iron ion transport / ferrous iron binding / cytoplasmic vesicle / intracellular iron ion homeostasis / 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
: / Ferritin light chain
Similarity search - Component
Biological speciesEQUUS CABALLUS (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsDe Val, N. / Declercq, J.P.
CitationJournal: J.Inorg.Biochem. / Year: 2012
Title: Structural Analysis of Haemin Demetallation by L-Chain Apoferritins
Authors: De Val, N. / Declercq, J.P. / Lim, C.K. / Crichton, R.R.
History
DepositionJun 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2May 30, 2012Group: Other
Revision 1.3Apr 10, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERRITIN LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,44315
Polymers19,9881
Non-polymers1,45614
Water2,540141
1
A: FERRITIN LIGHT CHAIN
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)514,642360
Polymers479,70224
Non-polymers34,940336
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
Buried area126790 Å2
ΔGint-534.5 kcal/mol
Surface area131490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.981, 182.981, 182.981
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-1002-

CD

21A-1172-

CD

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Components

#1: Protein FERRITIN LIGHT CHAIN / FERRITIN L SUBUNIT / RECOMBINANT HORSE L-CHAIN APOFERRITIN


Mass: 19987.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EQUUS CABALLUS (horse) / Organ: SPLEEN / Plasmid: PMK2100 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): BMH-71-18 / References: UniProt: P02791
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.2 Å3/Da / Density % sol: 61.5 % / Description: NONE
Crystal growpH: 8.2
Details: RESERVOIR: CADMIUM SULFATE 0.04M, AMMONIUM SULFATE 0.5M, SODIUM AZIDE 0.003M DROP: 1UL PROTEIN AND 1 UL RESERVOIR, pH 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 10, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→29 Å / Num. obs: 13290 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.7
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 9.3 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.3.0031refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V2I

2v2i


Resolution: 2.22→105.41 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.898 / SU B: 5.009 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 650 4.9 %RANDOM
Rwork0.186 ---
obs0.189 12639 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.12 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.22→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1363 0 43 141 1547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211415
X-RAY DIFFRACTIONr_bond_other_d0.0010.02979
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.9831898
X-RAY DIFFRACTIONr_angle_other_deg1.02332372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7455169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73924.32474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01315250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6581511
X-RAY DIFFRACTIONr_chiral_restr0.0970.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021557
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02289
X-RAY DIFFRACTIONr_nbd_refined0.2330.2287
X-RAY DIFFRACTIONr_nbd_other0.1960.2945
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2663
X-RAY DIFFRACTIONr_nbtor_other0.0920.2739
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4331.51094
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55721336
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.093654
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2824.5562
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.22→2.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.302 39
Rwork0.205 779

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