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- PDB-6l55: Recombinant Tegillarca granosa ferritin -

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Basic information

Entry
Database: PDB / ID: 6l55
TitleRecombinant 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
: / FORMIC ACID / Ferritin
Similarity search - Component
Biological speciesTegillarca granosa (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78304866205 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 6, 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.ptnr2_symmetry / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,80648
Polymers240,24512
Non-polymers1,56136
Water41,6332311
1
C: Ferritin
F: Ferritin
G: Ferritin
J: Ferritin
hetero molecules

C: Ferritin
F: Ferritin
G: Ferritin
J: Ferritin
hetero molecules

D: Ferritin
E: Ferritin
H: Ferritin
I: Ferritin
hetero molecules

D: Ferritin
E: Ferritin
H: Ferritin
I: Ferritin
hetero molecules

K: Ferritin
L: Ferritin
hetero molecules

K: Ferritin
L: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)483,61296
Polymers480,49124
Non-polymers3,12172
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x+1/2,-y-1/2,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation6_544-x+1/2,-y-1/2,z-11
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation8_445x-1/2,-y-1/2,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation7_545-x+1/2,y-1/2,-z1
Buried area104410 Å2
ΔGint-943 kcal/mol
Surface area130060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.623, 214.905, 151.902
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11D-436-

HOH

21D-490-

HOH

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Components

#1: Protein
Ferritin /


Mass: 20020.438 Da / Num. of mol.: 12
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.: 16 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2311 / 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: 3.69 Å3/Da / Density % sol: 66.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 4.0M Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 330028 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 9.09524895279 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 3.4
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 2 / Num. unique obs: 13365 / Rsym value: 0.158 / % possible all: 80.5

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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: 1BG7

1bg7


Resolution: 1.78304866205→48.0415875624 Å / SU ML: 0.155468541151 / Cross valid method: FREE R-VALUE / σ(F): 1.37501343695 / Phase error: 25.4898395884
RfactorNum. reflection% reflection
Rfree0.230925542471 16641 5.04661163441 %
Rwork0.203697445234 --
obs0.205079920377 329746 99.7573726055 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 8.94085098839 Å2
Refinement stepCycle: LAST / Resolution: 1.78304866205→48.0415875624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16584 0 54 2311 18949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053844650632417064
X-RAY DIFFRACTIONf_angle_d0.78092745598722951
X-RAY DIFFRACTIONf_chiral_restr0.0445268087932379
X-RAY DIFFRACTIONf_plane_restr0.004591502296723040
X-RAY DIFFRACTIONf_dihedral_angle_d14.594522306710416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7831-1.80330.2553630734075720.18631658848310212X-RAY DIFFRACTION97.9117486835
1.8033-1.82450.2169628130565030.18013814785210426X-RAY DIFFRACTION99.8629385965
1.8245-1.84680.2133044238545860.1743595889110323X-RAY DIFFRACTION99.9358739465
1.8468-1.87020.2129308573285350.17524239383910424X-RAY DIFFRACTION99.8633132859
1.8702-1.89480.2120476392575520.18244018800810349X-RAY DIFFRACTION99.826007326
1.8948-1.92070.2169991581495920.18510958326510406X-RAY DIFFRACTION99.8728659644
1.9207-1.94820.2390422144335460.1910463352310370X-RAY DIFFRACTION99.7806215722
1.9482-1.97720.2394552038775160.18484200477210405X-RAY DIFFRACTION99.8811048107
1.9772-2.00810.2013695601145680.17476988633210406X-RAY DIFFRACTION99.8725882781
2.0081-2.04110.2163017912375060.17624514982310360X-RAY DIFFRACTION99.889685604
2.0411-2.07630.2262893858375400.17884296497210437X-RAY DIFFRACTION99.908983344
2.0763-2.1140.2152046581165640.18125812111710425X-RAY DIFFRACTION99.9363404874
2.114-2.15470.1929615326525170.18029965153310385X-RAY DIFFRACTION99.9541578803
2.1547-2.19870.2274821268425600.19043910680810449X-RAY DIFFRACTION99.9636792881
2.1987-2.24650.2195883663465440.18535266154310426X-RAY DIFFRACTION99.9180253211
2.2465-2.29870.2203999307525670.19044548501310432X-RAY DIFFRACTION99.9454793276
2.2987-2.35620.2371512578765250.19474752482210414X-RAY DIFFRACTION99.8357214566
2.3562-2.41990.232467449235360.20119185618810448X-RAY DIFFRACTION99.8999545248
2.4199-2.49110.2294180117485840.20604580333510419X-RAY DIFFRACTION99.9545784884
2.4911-2.57150.2457426501285500.21222000777610461X-RAY DIFFRACTION99.9001996008
2.5715-2.66340.2507062021065680.21219486524710408X-RAY DIFFRACTION99.945365143
2.6634-2.770.2542863164566000.23547094514810411X-RAY DIFFRACTION99.9455387129
2.77-2.89610.2700747287484700.22391125005810531X-RAY DIFFRACTION99.8819684038
2.8961-3.04880.2514859040375480.23155690026910497X-RAY DIFFRACTION99.8734062754
3.0488-3.23970.232565065195680.22539367895110480X-RAY DIFFRACTION99.945721006
3.2397-3.48980.224794119655450.21955968793210462X-RAY DIFFRACTION99.7643433336
3.4898-3.84090.2649828198325470.22611163701510602X-RAY DIFFRACTION99.9462124608
3.8409-4.39630.2302792223026150.21157302558210472X-RAY DIFFRACTION99.7391147895
4.3963-5.53760.2244918671065810.21123543970610620X-RAY DIFFRACTION99.8217627662
5.5376-48.040.1967803453116360.21187044906110645X-RAY DIFFRACTION98.0530204259

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