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- PDB-6l58: Cu(II) loaded Tegillarca granosa M-ferritin soaked with Fe(II) -

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Basic information

Entry
Database: PDB / ID: 6l58
TitleCu(II) loaded Tegillarca granosa M-ferritin soaked with Fe(II)
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 / ferrous iron binding / intracellular iron ion homeostasis / cytoplasm
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
COPPER (II) ION / Ferritin
Similarity search - Component
Biological speciesTegillarca granosa (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.90270963518 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 / 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 / _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.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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,59012
Polymers80,0824
Non-polymers5088
Water181
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)483,54172
Polymers480,49124
Non-polymers3,05048
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area85350 Å2
ΔGint-870 kcal/mol
Surface area130510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.288, 217.288, 134.083
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11D-202-

CU

21D-203-

CU

31D-301-

HOH

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Components

#1: Protein
Ferritin


Mass: 20020.438 Da / Num. of mol.: 4
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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.8 Å3/Da / Density % sol: 67.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M ammonium acetate, 0.1M TRIS hydrochloride pH 7.5, a precipitant solution of 30% v/v 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.7389 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7389 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 10532 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 72.3114190968 Å2 / Rmerge(I) obs: 0.167 / Rsym value: 0.167 / Net I/σ(I): 10.357
Reflection shellResolution: 3.9→3.97 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 412 / CC1/2: 0.523 / % possible all: 73.4

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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: 3A9K

3a9k


Resolution: 3.90270963518→36.3993584617 Å / SU ML: 0.482757452022 / Cross valid method: FREE R-VALUE / σ(F): 1.34370859458 / Phase error: 30.8101531862
RfactorNum. reflection% reflection
Rfree0.263535661722 581 5.54072096128 %
Rwork0.186963347959 --
obs0.191065939557 10486 93.8764547896 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 65.1958603175 Å2
Refinement stepCycle: LAST / Resolution: 3.90270963518→36.3993584617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5153 0 8 1 5162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002623822202695256
X-RAY DIFFRACTIONf_angle_d0.503402368617148
X-RAY DIFFRACTIONf_chiral_restr0.035706453338779
X-RAY DIFFRACTIONf_plane_restr0.00280784595789962
X-RAY DIFFRACTIONf_dihedral_angle_d17.09443699233114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.90272-4.29490.3063601391481590.2103168595332380X-RAY DIFFRACTION91.6275712739
4.2949-4.91510.2476581981351670.1697327800192512X-RAY DIFFRACTION97.206095791
4.9151-6.18750.2820785304871370.208443008782582X-RAY DIFFRACTION97.735442128
6.1875-36.30090.2433611314181180.1731873795742431X-RAY DIFFRACTION89.0947221251

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