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- PDB-4cmy: Chlorobium tepidum Ferritin -

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Basic information

Entry
Database: PDB / ID: 4cmy
TitleChlorobium tepidum Ferritin
Components(FERRITIN) x 2
KeywordsMETAL TRANSPORT / IRON-STORAGE PROTEIN / IRON METABOLISM
Function / homology
Function and homology information


bacterial non-heme ferritin / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / cytosol
Similarity search - Function
Ferritin, prokaryotic-type / 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 ...Ferritin, prokaryotic-type / 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
Biological speciesCHLOROBACULUM TEPIDUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.59 Å
AuthorsPohl, E. / Arenas, M. / Townsend, P.D. / Yevenes, A.
CitationJournal: Biochimie / Year: 2014
Title: The Crystal Structure of Ferritin from Chlorobium Tepidum Reveals a New Conformation of the 4-Fold Channel for This Protein Family.
Authors: Arenas, M. / Townsend, P.D. / Brito, C. / Marquez, V. / Marabolli, V. / Gonzalez-Nilo, F. / Matias, C. / Watt, R.K. / Lopez-Castro, J.D. / Dominguez-Vera, J. / Pohl, E. / Yevenes, A.
History
DepositionJan 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.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.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.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_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
B: FERRITIN
C: FERRITIN
D: FERRITIN
E: FERRITIN
F: FERRITIN
G: FERRITIN
H: FERRITIN
I: FERRITIN
J: FERRITIN
K: FERRITIN
L: FERRITIN
M: FERRITIN
N: FERRITIN
O: FERRITIN
P: FERRITIN
Q: FERRITIN
R: FERRITIN
S: FERRITIN
T: FERRITIN
U: FERRITIN
V: FERRITIN
W: FERRITIN
X: FERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)566,54672
Polymers563,86624
Non-polymers2,68148
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area95540 Å2
ΔGint-1014.2 kcal/mol
Surface area141300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.310, 190.370, 242.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ...
FERRITIN


Mass: 23494.361 Da / Num. of mol.: 23
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLOROBACULUM TEPIDUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8KBP5
#2: Protein FERRITIN


Mass: 23495.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLOROBACULUM TEPIDUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8KBP5
#3: Chemical...
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.18 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.59→100 Å / Num. obs: 169035 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.15
Reflection shellResolution: 2.59→2.73 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.349 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.59→103.71 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.872 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.457 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21788 8723 4.9 %RANDOM
Rwork0.19297 ---
obs0.19421 169035 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.783 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å2-0 Å2
2---1.39 Å2-0 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.59→103.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31666 0 48 459 32173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01932535
X-RAY DIFFRACTIONr_bond_other_d0.010.0230335
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.92844074
X-RAY DIFFRACTIONr_angle_other_deg1.663369596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.54253927
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.26224.4581669
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.593155572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.51215144
X-RAY DIFFRACTIONr_chiral_restr0.0960.24874
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0236937
X-RAY DIFFRACTIONr_gen_planes_other0.0080.027969
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.586→2.653 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 629 -
Rwork0.288 12379 -
obs--99.9 %

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