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- PDB-3es3: Directing Noble Metal Ion Chemistry within a Designed Ferritin Pr... -

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Basic information

Entry
Database: PDB / ID: 3es3
TitleDirecting Noble Metal Ion Chemistry within a Designed Ferritin Protein. The Complex with Gold ions. Ferritin H8-H9x Mutant
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / Nanoparticle synthesis / gold ions / ferritin / mutant / Iron / Iron storage / Metal-binding / Phosphoprotein
Function / homology
Function and homology information


iron ion sequestering activity / intracellular ferritin complex / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / intracellular ferritin complex / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / ferrous iron binding / Iron uptake and transport / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / 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 iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / 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
: / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.795 Å
AuthorsDi Costanzo, L. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2008
Title: Directing noble metal ion chemistry within a designed ferritin protein.
Authors: Butts, C.A. / Swift, J. / Kang, S.G. / Di Costanzo, L. / Christianson, D.W. / Saven, J.G. / Dmochowski, I.J.
History
DepositionOct 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 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

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Assembly

Deposited unit
A: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9927
Polymers21,1241
Non-polymers8686
Water93752
1
A: Ferritin heavy chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)527,797168
Polymers506,96424
Non-polymers20,833144
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_545z,-y-1,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_545-z,-y-1,-x1
crystal symmetry operation29_545z,x-1/2,y+1/21
crystal symmetry operation30_544z,-x-1/2,-y-1/21
crystal symmetry operation31_545-z,-x-1/2,y+1/21
crystal symmetry operation32_544-z,x-1/2,-y-1/21
crystal symmetry operation41_544x,z-1/2,-y-1/21
crystal symmetry operation42_545-x,z-1/2,y+1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_545x,-z-1/2,y+1/21
crystal symmetry operation81_545y+1/2,z-1/2,x1
crystal symmetry operation82_445-y-1/2,z-1/2,-x1
crystal symmetry operation83_545y+1/2,-z-1/2,-x1
crystal symmetry operation84_445-y-1/2,-z-1/2,x1
crystal symmetry operation85_545y+1/2,x-1/2,-z1
crystal symmetry operation86_445-y-1/2,-x-1/2,-z1
crystal symmetry operation87_545y+1/2,-x-1/2,z1
crystal symmetry operation88_445-y-1/2,x-1/2,z1
MethodPQS
Unit cell
Length a, b, c (Å)181.564, 181.564, 181.564
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-734-

AU

21A-735-

CA

31A-736-

CA

41A-764-

HOH

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Components

#1: Protein Ferritin heavy chain / / Ferritin H subunit / Cell proliferation-inducing gene 15 protein


Mass: 21123.500 Da / Num. of mol.: 1
Mutation: H13D, E64C, K86Q, C90R, C102A, H105Q, C130S, E140C, K143C, E147C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli (E. coli) / References: UniProt: P02794, ferroxidase
#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Au
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Protein solution (11.0 mG/mL H8 in unbuffered 3.0MM NaN3), 2.5mL of precipitant buffer (0.1 M sodium acetate (PH 4.6), 20%(V/V) isopropanol, 0.2M CaCl2), VAPOR DIFFUSION, HANGING DROP, ...Details: Protein solution (11.0 mG/mL H8 in unbuffered 3.0MM NaN3), 2.5mL of precipitant buffer (0.1 M sodium acetate (PH 4.6), 20%(V/V) isopropanol, 0.2M CaCl2), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K. Soaking crystals were performed using a mother liquor (no calcium ions) with the addition of 0.5 mM AuCl3 for one week.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.98066 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98066 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 6736 / Num. obs: 6736 / % possible obs: 98.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 46.3 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 14.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
CNSrefinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2Z6M; one monomer

2z6m


Resolution: 2.795→34.942 Å / Occupancy max: 1 / Occupancy min: 0.19 / SU ML: 3.22 / σ(F): 0.13 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 229 3.7 %
Rwork0.2217 --
obs0.2237 6191 91.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.284 e/Å3
Displacement parametersBiso mean: 26.062 Å2
Baniso -1Baniso -2Baniso -3
1--5.318 Å2-0 Å2-0 Å2
2---5.318 Å2-0 Å2
3----5.318 Å2
Refinement stepCycle: LAST / Resolution: 2.795→34.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 6 52 1460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061429
X-RAY DIFFRACTIONf_angle_d0.9181926
X-RAY DIFFRACTIONf_dihedral_angle_d20.599527
X-RAY DIFFRACTIONf_chiral_restr0.065204
X-RAY DIFFRACTIONf_plane_restr0.003255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7953-3.52120.31751060.23042746X-RAY DIFFRACTION87
3.5212-34.94470.25161230.21693216X-RAY DIFFRACTION95

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