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

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Basic information

Entry
Database: PDB / ID: 3erz
TitleDirecting Noble Metal Ion Chemistry within a Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / ferritin mutant / nanoparticle / 3-fold channel / mercury ions / Iron / Iron storage / Metal-binding / Phosphoprotein
Function / homology
Function and homology information


iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / 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 / MOLECULAR REPLACEMENT / Resolution: 3.056 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: 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 / struct_conn ...database_2 / 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 / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,84243
Polymers253,68712
Non-polymers4,15431
Water3,729207
1
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)515,70984
Polymers507,37524
Non-polymers8,33460
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area98620 Å2
ΔGint-1292 kcal/mol
Surface area134470 Å2
MethodPISA
2
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules

G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules

G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules

G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)515,65888
Polymers507,37524
Non-polymers8,28364
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area103410 Å2
ΔGint-1430 kcal/mol
Surface area131930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.941, 170.941, 190.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-706-

ZN

21B-630-

MPD

31E-631-

MPD

41H-709-

ZN

51I-710-

ZN

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

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


Mass: 21140.615 Da / Num. of mol.: 12
Mutation: H13D, E64C, C90R, C102A, H105Q, E140C, K143C, E147C
Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02794, ferroxidase

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Non-polymers , 5 types, 238 molecules

#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.84 Å3/Da / Density % sol: 56.73 %
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 (0.1M 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 (0.1M sodium acetate (PH 4.6), 20%(v/v) isopropanol, 0.2M CaCl2), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K. Soaking experiment performed with mercury ions using the mother liquor without calcium ions.

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.98066 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98066 Å / Relative weight: 1
ReflectionResolution: 3.06→29 Å / Num. all: 47331 / Num. obs: 47331 / % possible obs: 88 % / Redundancy: 4.1 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.144 / Net I/σ(I): 9.6
Reflection shellResolution: 3.06→3.16 Å / Redundancy: 4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.7 / Num. unique all: 4847 / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
CNSrefinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.056→28.799 Å / Occupancy max: 1 / Occupancy min: 0.12 / SU ML: 3.27 / σ(F): 0.12 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 1895 4.1 %
Rwork0.199 44281 -
obs0.202 46176 85.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.445 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso max: 73.36 Å2 / Biso mean: 36.198 Å2 / Biso min: 10.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.344 Å20 Å20 Å2
2--0.344 Å20 Å2
3----0.688 Å2
Refinement stepCycle: LAST / Resolution: 3.056→28.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16836 0 20 295 17151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817241
X-RAY DIFFRACTIONf_angle_d1.23323222
X-RAY DIFFRACTIONf_chiral_restr0.0862448
X-RAY DIFFRACTIONf_plane_restr0.0073060
X-RAY DIFFRACTIONf_dihedral_angle_d21.6366393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.056-3.1320.3321380.2653049318785
3.132-3.2170.2541470.2333108325586
3.217-3.3120.3351520.2443108326086
3.312-3.4180.2981290.2283176330587
3.418-3.540.2961490.2043160330988
3.54-3.6820.2731100.1993215332588
3.682-3.8490.261310.1933233336488
3.849-4.0510.2251300.1673211334187
4.051-4.3040.2121340.1533176331087
4.304-4.6350.1781400.1573202334287
4.635-5.10.2211280.1673180330886
5.1-5.8320.2671580.1973118327684
5.832-7.3280.2961420.2113147328983
7.328-28.80.2061070.2083198330580

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