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- PDB-5up8: Crystal Structure of the Zn-bound Human Heavy-Chain variant 122H-... -

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Basic information

Entry
Database: PDB / ID: 5up8
TitleCrystal Structure of the Zn-bound Human Heavy-Chain variant 122H-delta C-star with para-benzenedihydroxamate
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / self-assembly / protein-MOF / protein-metal-organic framework
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 / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / iron ion transport / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm / cytosol
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 / Resolution: 2.631 Å
AuthorsBailey, J.B. / Zhang, L. / Chiong, J.C. / Ahn, S. / Tezcan, F.A.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Synthetic Modularity of Protein-Metal-Organic Frameworks.
Authors: Bailey, J.B. / Zhang, L. / Chiong, J.A. / Ahn, S. / Tezcan, F.A.
History
DepositionFeb 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Data collection / Database references / Refinement description
Category: citation / diffrn_detector / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_detector.detector / _software.version
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)21,5386
Polymers21,1221
Non-polymers4155
Water21612
1
A: Ferritin heavy chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)516,904144
Polymers506,93524
Non-polymers9,969120
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
Unit cell
Length a, b, c (Å)155.810, 155.810, 155.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-203-

ZN

21A-204-

NA

31A-303-

HOH

41A-310-

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
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.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.73 Å3/Da / Density % sol: 67.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Reservoir: 500 uL total volume: 50 mM CHES (pH 8.5), 150 mM NaCl, 0.14 mM ZnCl2 Sitting Drop: 8.6 uL reservoir, 1 uL of 12.5 uM ferritin, 2.4 uL of 5 mM p-H2bdh in 50 mM CHES (pH 9.5) with 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.63→49.27 Å / Num. obs: 9926 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.189 / Net I/σ(I): 12.5
Reflection shellResolution: 2.63→2.75 Å / Redundancy: 23 % / Rmerge(I) obs: 1.658 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1189 / CC1/2: 0.554 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.631→49.27 Å / Cross valid method: THROUGHOUT / σ(Fsqd): 1.35 / Phase error: 28.53
RfactorNum. reflection% reflection
Rfree0.262 492 -
Rwork0.209 9430 -
obs0.212 9922 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.87 Å2 / Biso mean: 84.5949 Å2 / Biso min: 47.02 Å2
Refinement stepCycle: LAST / Resolution: 2.631→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1403 0 18 12 1433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6307-2.89540.3411200.27423002420
2.8954-3.31430.29921190.237123092428
3.3143-4.17530.23481110.19923592470
4.1753-49.28010.2521420.193324622604
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.66530.27560.51071.0590.79211.2559-0.0071-0.49620.13770.28720.14870.1724-0.3704-0.360.4370.78070.1410.60911.2666-0.20180.7511-35.522310.819838.0058
20.0806-0.11570.5453.14160.64334.36880.2527-0.5701-0.24930.49830.1760.88540.0851-0.657-0.44410.5413-0.11130.26881.27650.10991.0721-46.815-9.293418.6206
31.12270.70011.02081.60440.97791.4016-0.0775-0.12550.14420.37940.46320.2253-0.26820.11940.07980.55050.07470.44991.0982-0.15580.7249-32.47277.318129.2954
40.75840.15640.18580.25660.04120.6179-0.0216-0.42020.15460.37040.01710.4631-0.0885-0.55590.12260.76170.18340.65681.3529-0.24751.0184-39.912214.071333.18
50.4464-0.8167-0.81932.03861.60242.39460.0398-0.06190.02030.1447-0.12860.7958-0.0812-0.8134-0.02490.29410.17820.24781.1134-0.06541.057-46.04858.127413.5681
63.79680.4350.49568.7164-0.81951.3687-0.0755-0.1143-1.04810.3307-0.38532.33170.4879-3.12350.46710.25330.00740.0950.67220.04660.6486-36.59824.927411.2066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 137 )
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 173 )
6X-RAY DIFFRACTION6chain 'A' and (resid 174 through 179 )

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