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- PDB-3a68: Crystal structure of plant ferritin reveals a novel metal binding... -

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Basic information

Entry
Database: PDB / ID: 3a68
TitleCrystal structure of plant ferritin reveals a novel metal binding site that functions as a transit site for metal transfer in ferritin
ComponentsFerritin-4, chloroplastic
KeywordsOXIDOREDUCTASE / 4-helix bundle / ferritin / iron storage / cage-like protein / plant / Chloroplast / Iron / Metal-binding / Plastid / Transit peptide
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / chloroplast / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
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 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
ACETIC ACID / Ferritin-4, chloroplastic
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMasuda, T. / Goto, F. / Yoshihara, T. / Mikami, B.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of plant ferritin reveals a novel metal binding site that functions as a transit site for metal transfer in ferritin
Authors: Masuda, T. / Goto, F. / Yoshihara, T. / Mikami, B.
History
DepositionAug 26, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: 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 / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

Downloads & links

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Assembly

Deposited unit
A: Ferritin-4, chloroplastic
B: Ferritin-4, chloroplastic
C: Ferritin-4, chloroplastic
D: Ferritin-4, chloroplastic
E: Ferritin-4, chloroplastic
F: Ferritin-4, chloroplastic
G: Ferritin-4, chloroplastic
H: Ferritin-4, chloroplastic
I: Ferritin-4, chloroplastic
J: Ferritin-4, chloroplastic
K: Ferritin-4, chloroplastic
L: Ferritin-4, chloroplastic
M: Ferritin-4, chloroplastic
N: Ferritin-4, chloroplastic
O: Ferritin-4, chloroplastic
P: Ferritin-4, chloroplastic
Q: Ferritin-4, chloroplastic
R: Ferritin-4, chloroplastic
S: Ferritin-4, chloroplastic
T: Ferritin-4, chloroplastic
U: Ferritin-4, chloroplastic
V: Ferritin-4, chloroplastic
W: Ferritin-4, chloroplastic
X: Ferritin-4, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)582,939178
Polymers576,40824
Non-polymers6,532154
Water81,3204514
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area134000 Å2
ΔGint-607 kcal/mol
Surface area150650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.610, 220.886, 122.452
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ...
Ferritin-4, chloroplastic / SFerH-4


Mass: 24016.986 Da / Num. of mol.: 24 / Fragment: UNP residues 36-247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q948P5, ferroxidase
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 136 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4514 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 15% PEG 1000, 0.2M calcium acetate, 0.1M imidazole, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Feb 12, 2009
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 552676 / Num. obs: 546597 / % possible obs: 98.9 % / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 13.15 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 7.96 / Num. unique all: 26571 / % possible all: 97.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Bullfrog M ferritin, PDB ENTRY 1MFR

1mfr


Resolution: 1.8→49.468 Å / SU ML: 0.18 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1727 27445 5.02 %RANDOM
Rwork0.1423 ---
all0.1439 553039 --
obs-546458 98.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.386 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso mean: 20.99 Å2
Baniso -1Baniso -2Baniso -3
1-5.5668 Å2-0 Å2-0 Å2
2---2.4738 Å2-0 Å2
3----3.0929 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å / Luzzati sigma a obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→49.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39263 0 208 4568 44039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00440301
X-RAY DIFFRACTIONf_angle_d0.77154691
X-RAY DIFFRACTIONf_dihedral_angle_d18.88315338
X-RAY DIFFRACTIONf_chiral_restr0.0545909
X-RAY DIFFRACTIONf_plane_restr0.0037287
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.820.228350.173163311716694
1.82-1.8420.2078840.171169091779397
1.842-1.8640.2119070.166169061781398
1.864-1.8880.2098710.162169901786197
1.888-1.9130.2069530.164169681792198
1.913-1.9390.1989390.158170191795898
1.939-1.9670.29080.155169901789898
1.967-1.9960.1979130.155171011801498
1.996-2.0270.1878750.142172221809799
2.027-2.060.1879410.145171421808399
2.06-2.0960.1839200.143171401806099
2.096-2.1340.1798970.142172581815599
2.134-2.1750.1799070.135172271813499
2.175-2.220.1779460.138171981814499
2.22-2.2680.1759040.138172881819299
2.268-2.320.1839010.14173191822099
2.32-2.3790.1729730.136172971827099
2.379-2.4430.1719500.138173401829099
2.443-2.5150.1749560.142172951825199
2.515-2.5960.179170.1471744118358100
2.596-2.6890.1768550.144174751833099
2.689-2.7960.1838760.1441750018376100
2.796-2.9240.1698830.1371754718430100
2.924-3.0780.1549180.1321750818426100
3.078-3.270.169420.1361754318485100
3.27-3.5230.1598780.1291763118509100
3.523-3.8770.1389190.121766018579100
3.877-4.4380.1299540.111769218646100
4.438-5.590.1449350.1281785218787100
5.59-49.4870.1829880.1661822419212100

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