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- PDB-2g4h: Anomalous substructure of apoferritin -

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Basic information

Entry
Database: PDB / ID: 2g4h
TitleAnomalous substructure of apoferritin
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / anomalous substructure of apoferritin
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 / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsMueller-Dieckmann, C. / Weiss, M.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths.
Authors: Mueller-Dieckmann, C. / Panjikar, S. / Schmidt, A. / Mueller, S. / Kuper, J. / Geerlof, A. / Wilmanns, M. / Singh, R.K. / Tucker, P.A. / Weiss, M.S.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICALLY SIGNIFICANT MOLECULE IS A HOLLOW, SPHERICAL SHELL MADE OF 24 PROTEIN CHAINS ARRANGED IN A 4 3 2 POINT SYMMETRY. A COMPLETE 24-MER (CENTERED AT X = 0, Y = 0, Z = 0) CAN BE GENERATED BY APPLYING THE 24 NON TRANSLATIONAL SYMMETRY OPERATIONS OF THE F 4 3 2 SPACE GROUP TO THE ASYMMETRICAL SUBUNIT BELOW.

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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)20,93912
Polymers19,8561
Non-polymers1,08311
Water1,820101
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)502,536288
Polymers476,55324
Non-polymers25,983264
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area98920 Å2
ΔGint-632 kcal/mol
Surface area134500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)182.160, 182.160, 182.160
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-201-

CD

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Components

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19856.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02791
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 3.17 Å3/Da / Density % sol: 61.2 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 18033 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
CCP4(SCALA)data scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.694 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21772 381 2.1 %RANDOM
Rwork0.19549 ---
obs0.19594 17652 99.81 %-
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: 25.213 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1363 0 11 101 1475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211387
X-RAY DIFFRACTIONr_bond_other_d0.0010.021258
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9681869
X-RAY DIFFRACTIONr_angle_other_deg0.90132920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70524.32474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69115250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8441511
X-RAY DIFFRACTIONr_chiral_restr0.0960.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021561
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02289
X-RAY DIFFRACTIONr_nbd_refined0.2650.2318
X-RAY DIFFRACTIONr_nbd_other0.1920.21144
X-RAY DIFFRACTIONr_nbtor_refined0.180.2682
X-RAY DIFFRACTIONr_nbtor_other0.0830.2758
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.4510.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3370.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2030.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1910.24
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6651.51101
X-RAY DIFFRACTIONr_mcbond_other0.2671.5350
X-RAY DIFFRACTIONr_mcangle_it1.9462.51338
X-RAY DIFFRACTIONr_scbond_it5.1635626
X-RAY DIFFRACTIONr_scangle_it7.1910531
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 29 -
Rwork0.229 1278 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å
111213212223313233
T0 Å20 Å20 Å2-0 Å20 Å2--0 Å2
L0 °20 °20 °2-0 °20 °2--0 °2
S0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °

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