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- PDB-6kzy: Cu(II) loaded Tegillarca granosa ferritin -

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Basic information

Entry
Database: PDB / ID: 6kzy
TitleCu(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 / 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 / ISOPROPYL ALCOHOL / Ferritin
Similarity search - Component
Biological speciesTegillarca granosa (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.30057069642 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
DepositionSep 25, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,80354
Polymers80,0824
Non-polymers1,72250
Water7,224401
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)490,820324
Polymers480,49124
Non-polymers10,329300
Water43224
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 area104800 Å2
ΔGint-671 kcal/mol
Surface area131080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.054, 217.054, 132.874
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
11C-202-

CU

21C-203-

CU

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 451 molecules

#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: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.83 Å3/Da / Density % sol: 67.88 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Ammonium acetate, 0.1M TRIS hydrochloride pH 7.5
PH range: 7.05-8.0

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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: Dec 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7389 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 51876 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 27.9518521689 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 32.604
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 21.456 / Num. unique obs: 2630 / Rsym value: 0.218 / % possible all: 100

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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: 3A9Q

3a9q


Resolution: 2.30057069642→32.7214665914 Å / SU ML: 0.209776178195 / Cross valid method: FREE R-VALUE / σ(F): 1.34754354108 / Phase error: 17.1564081342
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.194555703163 2574 4.96307579585 %
Rwork0.152139865928 49289 -
obs0.154153127908 51863 97.7495900635 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.9761898167 Å2
Refinement stepCycle: LAST / Resolution: 2.30057069642→32.7214665914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5506 0 69 401 5976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006370080662435687
X-RAY DIFFRACTIONf_angle_d0.7342255965497645
X-RAY DIFFRACTIONf_chiral_restr0.0405769111508786
X-RAY DIFFRACTIONf_plane_restr0.004498434571851009
X-RAY DIFFRACTIONf_dihedral_angle_d18.04064903733465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3006-2.34480.2077366924351560.1616715657322756X-RAY DIFFRACTION99.9313658202
2.3448-2.39270.2193534155451570.1520661672452783X-RAY DIFFRACTION99.9659979599
2.3927-2.44470.2854392356921610.1600074684622780X-RAY DIFFRACTION100
2.4447-2.50150.1870003800171610.1549225699972745X-RAY DIFFRACTION100
2.5015-2.5640.1822963216251890.147478677282742X-RAY DIFFRACTION100
2.564-2.63330.2421651314041660.1415244532772759X-RAY DIFFRACTION99.96582365
2.6333-2.71080.2107044416511290.1516413309422833X-RAY DIFFRACTION99.8988195616
2.7108-2.79820.1861944037091160.1503274742552765X-RAY DIFFRACTION99.9653018737
2.7982-2.89820.1861683281531910.1471488920642776X-RAY DIFFRACTION100
2.8982-3.01420.2262945029131090.1473780919612840X-RAY DIFFRACTION100
3.0142-3.15120.2308964734781210.1555679582832817X-RAY DIFFRACTION100
3.1512-3.31720.268182859591840.1615136964352842X-RAY DIFFRACTION100
3.3172-3.52480.1861653686361560.1636760674212745X-RAY DIFFRACTION98.707043212
3.5248-3.79660.174438608731860.1694455250962096X-RAY DIFFRACTION73.2706514439
3.7966-4.1780.1630634377041320.1446204375942502X-RAY DIFFRACTION88.9564336373
4.178-4.7810.2056203224461660.1279791471272775X-RAY DIFFRACTION99.9660095173
4.781-6.01740.1825711198881590.158411620692812X-RAY DIFFRACTION99.8991257566
6.0174-32.62480.19461350.15212921X-RAY DIFFRACTION99.3821138211

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