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- PDB-5cmq: Crystal Structure of Zn-bound Human H-Ferritin variant 122H-delta... -

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Basic information

Entry
Database: PDB / ID: 5cmq
TitleCrystal Structure of Zn-bound Human H-Ferritin variant 122H-delta C-star
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / Protein Engineering / Metal Binding
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
Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.935 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 30, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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_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

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Assembly

Deposited unit
A: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,71110
Polymers21,1221
Non-polymers5899
Water4,306239
1
A: Ferritin heavy chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)521,063240
Polymers506,93524
Non-polymers14,128216
Water43224
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
Buried area92500 Å2
ΔGint-287 kcal/mol
Surface area140500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.210, 180.210, 180.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-203-

ZN

21A-204-

ZN

31A-205-

ZN

41A-206-

ZN

51A-207-

ZN

61A-319-

HOH

71A-519-

HOH

81A-520-

HOH

91A-531-

HOH

101A-534-

HOH

111A-539-

HOH

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Components

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


Mass: 21122.291 Da / Num. of mol.: 1
Fragment: Ferritin-like diiron domain containing residues 6-177
Mutation: K86Q, 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.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25 mM Tris, 10 mM calcium chloride, 10 mM zinc chloride, 2% PEG 3350

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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 4, 2014
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: 1.935→104.044 Å / Num. all: 17713 / Num. obs: 17713 / % possible obs: 91.7 % / Redundancy: 13.7 % / Rpim(I) all: 0.027 / Rrim(I) all: 0.101 / Rsym value: 0.097 / Net I/av σ(I): 6.333 / Net I/σ(I): 19.2 / Num. measured all: 242003
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
1.93-2.0414.20.32873290623120.090.328784
2.04-2.1613.10.2732.22931922450.0790.2739.286.2
2.16-2.3113.60.2142.82868821150.0610.21411.886.2
2.31-2.514.40.1345.33301722980.0360.13415.4100
2.5-2.74130.1285.32531019460.0360.1281791.7
2.74-3.0614.50.08482798219340.0230.08423.4100
3.06-3.5313.20.0728.92137616210.0210.07229.493.8
3.53-4.3314.30.05710.71924913420.0160.0573890.3
4.33-6.12130.05211.91534211820.0150.05234.799.9
6.12-31.85712.30.03914.688147180.0110.03933.999.1

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Processing

Software
NameVersionClassification
PDB_EXTRACTdata extraction
REFMAC5.8.0123refinement
Cootmodel building
MOLREPphasing
SCALAdata scaling
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CEI

2cei


Resolution: 1.935→104.04 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.389 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1802 806 4.6 %RANDOM
Rwork0.1408 ---
obs0.1426 16841 91.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.97 Å2 / Biso mean: 16.52 Å2 / Biso min: 8.22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.935→104.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1417 0 9 239 1665
Biso mean--31.93 27.89 -
Num. residues----172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191449
X-RAY DIFFRACTIONr_bond_other_d0.0060.021337
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.9311958
X-RAY DIFFRACTIONr_angle_other_deg1.05933067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.465175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.64125.23386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7915255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.204157
X-RAY DIFFRACTIONr_chiral_restr0.1260.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021691
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02362
X-RAY DIFFRACTIONr_mcbond_it1.4331.348691
X-RAY DIFFRACTIONr_mcbond_other1.3571.344690
X-RAY DIFFRACTIONr_mcangle_it2.0392.007863
LS refinement shellResolution: 1.935→1.985 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 39 -
Rwork0.196 885 -
all-924 -
obs--67.35 %

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