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- PDB-2za6: recombinant horse L-chain apoferritin -

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Basic information

Entry
Database: PDB / ID: 2za6
Titlerecombinant horse L-chain apoferritin
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / ferric iron binding / Acetylation / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsYamashita, I. / Mishima, Y. / Park, S.-Y. / Heddle, J.G. / Tame, J.R.H.
CitationJournal: J.BIOCHEM.(TOKYO) / Year: 2007
Title: Effect of N-terminal Residues on the Structural Stability of Recombinant Horse L-chain Apoferritin in an Acidic Environment
Authors: Yoshizawa, K. / Mishima, Y. / Park, S.-Y. / Heddle, J.G. / Tame, J.R.H. / Iwahori, K. / Kobayashi, M. / Yamashita, I.
History
DepositionOct 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2123
Polymers19,9881
Non-polymers2252
Water3,135174
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)485,09872
Polymers479,70224
Non-polymers5,39648
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation29_554z,x+1/2,y-1/21
crystal symmetry operation41_555x,z+1/2,-y+1/21
crystal symmetry operation44_554x,-z+1/2,y-1/21
crystal symmetry operation30_555z,-x+1/2,-y+1/21
crystal symmetry operation87_455y-1/2,-x+1/2,z1
crystal symmetry operation84_555-y+1/2,-z+1/2,x1
crystal symmetry operation88_555-y+1/2,x+1/2,z1
crystal symmetry operation81_455y-1/2,z+1/2,x1
crystal symmetry operation85_455y-1/2,x+1/2,-z1
crystal symmetry operation82_555-y+1/2,z+1/2,-x1
crystal symmetry operation4_565x,-y+1,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation86_555-y+1/2,-x+1/2,-z1
crystal symmetry operation83_455y-1/2,-z+1/2,-x1
crystal symmetry operation31_554-z,-x+1/2,y-1/21
crystal symmetry operation43_555-x,-z+1/2,-y+1/21
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation42_554-x,z+1/2,y-1/21
crystal symmetry operation32_555-z,x+1/2,-y+1/21
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation24_565-z,-y+1,-x1
Buried area103570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.452, 180.452, 180.452
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432

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Components

#1: Protein Ferritin light chain / L ferritin / Ferritin L subunit


Mass: 19987.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Plasmid: PMK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P02791
#2: Chemical ChemComp-CD / CADMIUM ION


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


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEE REF. 2 IN THE DATABASE, P02791 IN UNP.

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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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris-HCl, 0.13% cadmium chloride, 15% PEG4000, 19 mM calcium chloride, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→99 Å / Num. obs: 25894 / % possible obs: 99.7 % / Biso Wilson estimate: 9.8 Å2

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AEW

1aew


Resolution: 1.75→19.8 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.909 / SU B: 1.711 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22523 1247 4.8 %RANDOM
Rwork0.19513 ---
obs0.19658 24602 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.703 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1369 0 2 174 1545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211392
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9641875
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6765170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021063
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.2681
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2138
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.71.5846
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38321344
X-RAY DIFFRACTIONr_scbond_it2.5513546
X-RAY DIFFRACTIONr_scangle_it4.3474.5531
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.223 94
Rwork0.209 1739

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