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- PDB-2v2s: Mutant R59M recombinant horse spleen apoferritin crystallized in ... -

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Basic information

Entry
Database: PDB / ID: 2v2s
TitleMutant R59M recombinant horse spleen apoferritin crystallized in acidic conditions
ComponentsFERRITIN LIGHT CHAIN
KeywordsMETAL TRANSPORT / IRON / IRON STORAGE / METAL-BINDING
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
: / Ferritin light chain
Similarity search - Component
Biological speciesEQUUS CABALLUS (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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 / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 30, 2012Group: Other
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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)21,01012
Polymers19,8301
Non-polymers1,18011
Water4,864270
1
A: FERRITIN LIGHT CHAIN
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)504,238288
Polymers475,92924
Non-polymers28,309264
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 area109210 Å2
ΔGint-577.7 kcal/mol
Surface area135080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.242, 181.242, 181.242
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-1171-

CD

21A-1172-

CD

31A-2214-

HOH

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Components

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


Mass: 19830.387 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EQUUS CABALLUS (horse) / Organ: SPLEEN / Plasmid: PMK2100 / Production host: ESCHERICHIA COLI (E. coli) / Strain (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.: 2 / 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.: 270 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 59 TO MET

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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: 3.1 Å3/Da / Density % sol: 60.4 % / Description: NONE
Crystal growpH: 5.5
Details: RESERVOIR: CADMIUM SULFATE 0.12M, AMMONIUM SULFATE 1.1M, SODIUM ACETATE 0.1M PH5.6, SODIUM AZIDE 0.003M. DROP: 1UL PROTEIN AND 1UL RESERVOIR, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8088
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 27, 2007 / Details: MIRROR 2 BENT, VERTICALLY FOCUSSING
RadiationMonochromator: SI 111, HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8088 Å / Relative weight: 1
ReflectionResolution: 1.37→23 Å / Num. obs: 53821 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15
Reflection shellResolution: 1.37→1.5 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 4.2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.3.0031refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V2N

2v2n


Resolution: 1.37→104.83 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.144 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2735 5.1 %RANDOM
Rwork0.202 ---
obs0.203 51086 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.32 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.37→104.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 25 270 1661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211412
X-RAY DIFFRACTIONr_bond_other_d0.0030.02963
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.9771901
X-RAY DIFFRACTIONr_angle_other_deg1.09732341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0155172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72224.52173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01815253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3431510
X-RAY DIFFRACTIONr_chiral_restr0.1280.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021573
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
X-RAY DIFFRACTIONr_nbd_refined0.2610.2323
X-RAY DIFFRACTIONr_nbd_other0.2030.2973
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2691
X-RAY DIFFRACTIONr_nbtor_other0.0880.2719
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2158
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.380.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7461.51110
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81621355
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5813641
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9644.5546
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: 1.37→1.41 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.371 210
Rwork0.389 3703

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