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- PDB-2v2i: Wild type recombinant horse spleen apoferritin cocrystallized wit... -

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Basic information

Entry
Database: PDB / ID: 2v2i
TitleWild type recombinant horse spleen apoferritin cocrystallized with haemin in acidic conditions
ComponentsFERRITIN LIGHT CHAIN
KeywordsMETAL TRANSPORT / IRON / HAEMIN / APOFERRITIN / IRON STORAGE / METAL-BINDING
Function / homology
Function and homology information


ferritin complex / autolysosome / ferric iron binding / autophagosome / ferrous iron binding / iron ion transport / 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 / Ferritin, core subunit, four-helix bundle / 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 / Ferritin, core subunit, four-helix bundle / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 / Non-polymer description / Other / 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)21,07511
Polymers19,9881
Non-polymers1,08710
Water3,531196
1
A: FERRITIN LIGHT CHAIN
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)505,801264
Polymers479,70224
Non-polymers26,099240
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 area104940 Å2
ΔGint-483 kcal/mol
Surface area134340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.334, 182.334, 182.334
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.: 1 / 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.: 196 / 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 % / Description: NONE
Crystal growpH: 5.5
Details: RESERVOIR: CADMIUM SULFATE 0.13M, AMMONIUM SULFATE 0.8M, SODIUM ACETATE 0.1M PH 5.5, SODIUM AZIDE 0.003M DROP 2 UL PROTEIN AND 2UL RESERVOIR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97991
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 14, 2003 / Details: TWO MIRRORS ARE USED FOR VERTICAL FOCUSSING.
RadiationMonochromator: FIRST CRYSTAL FLAT AND N2 COOLED. SECOND ONE SAGITALLY BENT. SI(111) OR SI(311)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97991 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 18049 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 32.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 6.2 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.3.0031refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HRS

1hrs


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.926 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 919 5.2 %RANDOM
Rwork0.177 ---
obs0.179 16869 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1363 0 19 196 1578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211395
X-RAY DIFFRACTIONr_bond_other_d0.0010.02955
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9721878
X-RAY DIFFRACTIONr_angle_other_deg0.95132316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6415169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51724.32474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72815250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6141511
X-RAY DIFFRACTIONr_chiral_restr0.1130.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.021557
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02289
X-RAY DIFFRACTIONr_nbd_refined0.2580.3291
X-RAY DIFFRACTIONr_nbd_other0.2130.3952
X-RAY DIFFRACTIONr_nbtor_refined0.190.5664
X-RAY DIFFRACTIONr_nbtor_other0.0940.5720
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.5208
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3340.36
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.350
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.543
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6441.51097
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.53121336
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.2443632
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.1684.5542
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→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.276 50
Rwork0.187 1196

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