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- PDB-6l56: Fe(II) loaded Tegillarca granosa ferritin -

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Basic information

Entry
Database: PDB / ID: 6l56
TitleFe(II) loaded Tegillarca granosa ferritin
ComponentsFerritin
KeywordsOXIDOREDUCTASE / ferritin / copper / tegillarca granosa / Structural Genomics / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis
Similarity search - Function
Ferritin iron-binding regions signature 1. / 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 iron-binding regions signature 1. / 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
Biological speciesTegillarca granosa (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85300580472 Å
AuthorsJiang, Q.Q. / Su, X.R. / Ming, T.H. / Huan, H.S.
CitationJournal: Front Mol Biosci / Year: 2022
Title: Structural Insights Into the Effects of Interactions With Iron and Copper Ions on Ferritin From the Blood Clam Tegillarca granosa.
Authors: Ming, T.H. / Jiang, Q.Q. / Huo, C. / Huan, H.S. / Wu, Y. / Su, C. / Qiu, X. / Lu, C. / Zhou, J. / Li, Y. / Han, J. / Zhang, Z. / Su, X.R.
History
DepositionOct 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_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.ptnr1_symmetry / _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_conn.ptnr2_symmetry
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)485,339132
Polymers480,49124
Non-polymers4,848108
Water48,9832719
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100690 Å2
ΔGint-1187 kcal/mol
Surface area132830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.900, 182.000, 182.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number16
Space group name H-MP222
Space group name HallP22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-205-

NA

21D-203-

NA

31F-203-

NA

41G-202-

NA

51J-203-

NA

61L-203-

NA

71M-203-

NA

81O-203-

NA

91R-203-

NA

101S-203-

NA

111V-203-

NA

121X-203-

NA

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Components

#1: Protein ...
Ferritin /


Mass: 20020.438 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tegillarca granosa (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D3JCC5, ferroxidase
#2: Chemical...
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2719 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M sodium cacodylate trihydrate pH 6.5, 30% v/v (+/-)-2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97892 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 505323 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 12.36317743 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.062 / Rrim(I) all: 0.158 / Rsym value: 0.145 / Χ2: 0.785 / Net I/av σ(I): 11.429 / Net I/σ(I): 11.429
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 1.833 / Num. unique obs: 24901 / CC1/2: 0.798 / Rpim(I) all: 0.34 / Rrim(I) all: 0.798 / Rsym value: 0.718 / Χ2: 0.446 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
xia2data reduction
HKL-3000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RCD

1rcd


Resolution: 1.85300580472→44.1186557677 Å / SU ML: 0.168946357154 / Cross valid method: FREE R-VALUE / σ(F): 1.96425499726 / Phase error: 17.9486605964
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.195768369097 25630 5.07822406797 %
Rwork0.16521311816 479074 -
obs0.166751590386 504704 99.4898401709 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.2235201556 Å2
Refinement stepCycle: LAST / Resolution: 1.85300580472→44.1186557677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32827 0 108 2719 35654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059762674374833451
X-RAY DIFFRACTIONf_angle_d0.731809417644987
X-RAY DIFFRACTIONf_chiral_restr0.04750760126414700
X-RAY DIFFRACTIONf_plane_restr0.004229442530345924
X-RAY DIFFRACTIONf_dihedral_angle_d14.0450898420400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8534-1.87410.2618135016087820.21629792730515420X-RAY DIFFRACTION96.3601760438
1.8741-1.89610.2308150011518290.20251556627515712X-RAY DIFFRACTION98.646230916
1.8961-1.91920.2395813671098920.1940363758315781X-RAY DIFFRACTION99.2381405869
1.9192-1.94350.2414235467668960.18930739552515734X-RAY DIFFRACTION99.2480305562
1.9435-1.96910.2325242906518890.1795291805715822X-RAY DIFFRACTION99.4288094246
1.9691-1.99610.2301407157218470.17127405701915840X-RAY DIFFRACTION99.015012164
1.9961-2.02460.2005283969617940.16841780503315870X-RAY DIFFRACTION99.1609639988
2.0246-2.05480.2001514939599390.17083833315515773X-RAY DIFFRACTION99.6185026228
2.0548-2.08690.2056994708367760.1617821388915936X-RAY DIFFRACTION99.6482022539
2.0869-2.12110.2073209208658410.15939937034915920X-RAY DIFFRACTION99.5308788599
2.1211-2.15770.1963538961697540.15649882312216005X-RAY DIFFRACTION99.809421714
2.1577-2.19690.1894561981768440.1585340762315997X-RAY DIFFRACTION99.692180193
2.1969-2.23920.1986298065127930.16177172330116018X-RAY DIFFRACTION99.8693043427
2.2392-2.28490.1854896439688030.15280935153216030X-RAY DIFFRACTION99.7806757558
2.2849-2.33460.1966059354378450.1675806493915893X-RAY DIFFRACTION99.7913313063
2.3346-2.38890.2183578512537590.15752527535516080X-RAY DIFFRACTION99.928787609
2.3889-2.44860.1860078117159200.17044354605815985X-RAY DIFFRACTION99.8405386251
2.4486-2.51480.2049409268349210.17115581003815862X-RAY DIFFRACTION99.9226006192
2.5148-2.58880.2063848255919050.16656657778115944X-RAY DIFFRACTION99.928829844
2.5888-2.67240.1956545625799660.16676480923615947X-RAY DIFFRACTION99.9645369112
2.6724-2.76790.2048959633438480.1752178835816172X-RAY DIFFRACTION99.9530185577
2.7679-2.87870.1982485878048130.16766034792615915X-RAY DIFFRACTION99.9820692128
2.8787-3.00960.1991393791018340.16976895115116087X-RAY DIFFRACTION99.9468399291
3.0096-3.16830.2000138622167660.16928448054116220X-RAY DIFFRACTION99.9705726561
3.1683-3.36670.2052388318539250.16907417837516080X-RAY DIFFRACTION99.9588525747
3.3667-3.62660.1888250775318360.16069283039416160X-RAY DIFFRACTION99.9470743899
3.6266-3.99130.18791266428430.15348801387716191X-RAY DIFFRACTION99.9589225984
3.9913-4.56830.1435491394259420.13384551545316164X-RAY DIFFRACTION99.9415751344
4.5683-5.75360.1706656672298860.15857665060616325X-RAY DIFFRACTION99.8839301259
5.7536-44.110.1770661400839420.17021646237416191X-RAY DIFFRACTION96.8349064602

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