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- PDB-5cmr: Crystal Structure of Linker-Mediated Zn-bound Human H-Ferritin va... -

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Basic information

Entry
Database: PDB / ID: 5cmr
TitleCrystal Structure of Linker-Mediated Zn-bound Human H-Ferritin variant 122H-delta C-star
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / Protein Engineering / Metal Binding / Supramolecular Assembly
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / autophagosome / ferric iron binding / Iron uptake and transport / ferrous iron binding / 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 / membrane / 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
N,N'-dihydroxybenzene-1,4-dicarboxamide / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.792 Å
AuthorsSontz, P.A. / Bailey, J.B. / Ahn, S. / Tezcan, F.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-10ER46677 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: A Metal Organic Framework with Spherical Protein Nodes: Rational Chemical Design of 3D Protein Crystals.
Authors: Sontz, P.A. / Bailey, J.B. / Ahn, S. / Tezcan, F.A.
History
DepositionJul 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Derived calculations
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_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.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.value / _struct_conn.pdbx_dist_value / _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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4617
Polymers21,0651
Non-polymers3966
Water00
1
A: Ferritin heavy chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)515,069168
Polymers505,56624
Non-polymers9,503144
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Unit cell
Length a, b, c (Å)155.320, 155.320, 155.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-202-

ZN

21A-203-

NA

31A-204-

NA

41A-206-

BYD

51A-206-

BYD

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Components

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


Mass: 21065.240 Da / Num. of mol.: 1
Fragment: Ferritin-like diiron domain containing residues 6-178
Mutation: K86A, C90E, C102A, C130A, T122H
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-BYD / N,N'-dihydroxybenzene-1,4-dicarboxamide


Mass: 196.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N2O4

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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: 3.71 Å3/Da / Density % sol: 66.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 50 mM CHES, 150 mM sodium chloride, 0.3 mM zinc chloride, 1 mM H2BDH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2015
RadiationMonochromator: Rh coated flat mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.792→109.828 Å / Num. all: 3401 / Num. obs: 3401 / % possible obs: 99.8 % / Redundancy: 11.2 % / Biso Wilson estimate: 94.54 Å2 / Rpim(I) all: 0.056 / Rrim(I) all: 0.194 / Rsym value: 0.185 / Net I/av σ(I): 4.125 / Net I/σ(I): 12 / Num. measured all: 38132
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
3.79-412.10.555557984810.1620.5555100
4-4.2411.20.3921.950964570.1190.3926.7100
4.24-4.5310.20.3272.343114210.1030.3277.499.7
4.53-4.89120.2622.948994070.0770.2629.7100
4.89-5.3611.60.2323.343883780.0690.23210.499.9
5.36-5.9910.30.2393.235013390.0750.2399.299.7
5.99-6.9212.10.1754.337023060.0520.17512.9100
6.92-8.47110.0987.429222650.030.09821.699.5
8.47-11.9910.70.04813.822892130.0160.04832.599.7
11.99-54.9149.10.03215.712261340.0110.0323596.9

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Processing

Software
NameVersionClassification
PDB_EXTRACTdata extraction
PHENIX(phenix.refine: 1.9_1692)refinement
Cootmodel building
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CEI

2cei


Resolution: 3.792→54.914 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 345 10.15 %
Rwork0.2074 3055 -
obs0.2124 3400 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.88 Å2 / Biso mean: 81.9409 Å2 / Biso min: 47.02 Å2
Refinement stepCycle: final / Resolution: 3.792→54.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1421 0 27 0 1448
Biso mean--71.17 --
Num. residues----173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051465
X-RAY DIFFRACTIONf_angle_d1.0671974
X-RAY DIFFRACTIONf_chiral_restr0.046204
X-RAY DIFFRACTIONf_plane_restr0.007263
X-RAY DIFFRACTIONf_dihedral_angle_d17.312554
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.7917-4.77670.28541670.220614881655100
4.7767-54.91960.23741780.19941567174599

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