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- PDB-6wyh: Crystal structure of Human H-chain Ferritin variant 157C Delta C-... -

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Basic information

Entry
Database: PDB / ID: 6wyh
TitleCrystal structure of Human H-chain Ferritin variant 157C Delta C-star Modified with a RAFT Agent Soaked in an Acrylate Solution
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / Ferritin / Polymer / Hydrogel / Polymer Integrated Crystals / Crystal Hydrogel Hybrids / RAFT Polymerization
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / 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 / membrane / cytosol / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin, core subunit, four-helix bundle / 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 / Ferritin, core subunit, four-helix bundle / 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
: / Chem-RFT / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsBailey, J.B. / Zhang, L.
Citation
Journal: J.Am.Chem.Soc. / Year: 2020
Title: Anisotropic Dynamics and Mechanics of Macromolecular Crystals Containing Lattice-Patterned Polymer Networks.
Authors: Han, K. / Bailey, J.B. / Zhang, L. / Tezcan, F.A.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionMay 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_seq_num

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,58225
Polymers84,2374
Non-polymers2,34521
Water12,520695
1
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)519,492150
Polymers505,42124
Non-polymers14,071126
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area98960 Å2
ΔGint-1076 kcal/mol
Surface area144800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.880, 128.880, 291.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11D-203-

CA

21D-204-

CA

31B-487-

HOH

41D-421-

HOH

51D-443-

HOH

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Components

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


Mass: 21059.211 Da / Num. of mol.: 4 / Mutation: K86Q, C90E, C102A, C130A, K157C
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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-RFT / butyl 1-{[2-(2,5-dioxopyrrolidin-1-yl)ethyl]amino}-2-methyl-1-oxopropan-2-yl carbonotrithioate


Mass: 376.558 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O3S3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 5 uL reservoir + 5 uL of 25 uM 157C delta C-star Human H-chain Ferritin in 15 mM HEPES, pH 7.0 against reservoir of 500 uL 50 mM MES, pH 6.5, 6 mM calcium chloride; crystals soaked in 1 M ...Details: 5 uL reservoir + 5 uL of 25 uM 157C delta C-star Human H-chain Ferritin in 15 mM HEPES, pH 7.0 against reservoir of 500 uL 50 mM MES, pH 6.5, 6 mM calcium chloride; crystals soaked in 1 M sodium acrylate, 50 mM calcium chloride, 25 mM MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.22→97.27 Å / Num. obs: 46081 / % possible obs: 99.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 20.66 Å2 / CC1/2: 0.972 / Net I/σ(I): 4.4
Reflection shellResolution: 2.22→2.29 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4179 / CC1/2: 0.571 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6B8F

6b8f


Resolution: 2.22→97.27 Å / SU ML: 0.2767 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.0813
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2452 4643 10.21 %
Rwork0.1932 40828 -
obs0.1985 45471 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.11 Å2
Refinement stepCycle: LAST / Resolution: 2.22→97.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5612 0 53 695 6360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00355812
X-RAY DIFFRACTIONf_angle_d0.61337862
X-RAY DIFFRACTIONf_chiral_restr0.039826
X-RAY DIFFRACTIONf_plane_restr0.00331052
X-RAY DIFFRACTIONf_dihedral_angle_d9.8631782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.250.48911140.52681189X-RAY DIFFRACTION85.5
2.25-2.270.66161370.55761163X-RAY DIFFRACTION85.02
2.27-2.30.48391420.45411243X-RAY DIFFRACTION90.94
2.3-2.330.31321240.25471380X-RAY DIFFRACTION98.69
2.33-2.360.26291330.21291398X-RAY DIFFRACTION98.84
2.36-2.390.28071350.19641374X-RAY DIFFRACTION99.54
2.39-2.430.26311540.20191376X-RAY DIFFRACTION99.8
2.43-2.460.32511790.21141335X-RAY DIFFRACTION99.87
2.46-2.50.27861700.19711375X-RAY DIFFRACTION99.55
2.5-2.540.27591610.19981365X-RAY DIFFRACTION99.48
2.54-2.590.23211470.19071374X-RAY DIFFRACTION99.8
2.59-2.630.2781540.19361374X-RAY DIFFRACTION99.74
2.63-2.680.29431540.19931372X-RAY DIFFRACTION99.09
2.68-2.740.26781540.20061360X-RAY DIFFRACTION98.44
2.74-2.80.26981530.20331372X-RAY DIFFRACTION99.35
2.8-2.860.28021680.19991362X-RAY DIFFRACTION99.22
2.86-2.930.22641460.18941386X-RAY DIFFRACTION99.67
2.93-3.010.26461330.18471398X-RAY DIFFRACTION99.35
3.01-3.10.25911460.18371386X-RAY DIFFRACTION99.8
3.1-3.20.24561680.17571362X-RAY DIFFRACTION99.67
3.2-3.320.2231710.17141382X-RAY DIFFRACTION99.81
3.32-3.450.22391810.17361338X-RAY DIFFRACTION98.96
3.45-3.610.22141760.15841378X-RAY DIFFRACTION98.67
3.61-3.80.21761580.17131355X-RAY DIFFRACTION98.25
3.8-4.030.1911600.14611379X-RAY DIFFRACTION98.91
4.03-4.350.16661530.12311401X-RAY DIFFRACTION99.81
4.35-4.780.17381730.12091381X-RAY DIFFRACTION98.92
4.78-5.470.16921600.14021388X-RAY DIFFRACTION98.47
5.48-6.90.19731650.17841412X-RAY DIFFRACTION99
6.9-97.270.21271740.18621470X-RAY DIFFRACTION97.86
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)
11.000647947310.7455764029530.1894127694621.238055836170.0207322197283-0.03726355950770.0536113747207-0.2653340068350.02757390490370.271633864265-0.0590893284076-0.068541727359-0.00805031648562-0.0139089241856-0.0341325254940.2939634940430.0127577976437-0.02238642143190.270595403169-0.05389358164920.1697698523211.6647510324923.256179868846.4413565872
28.245207901763.9156867622-6.285950646992.12629229886-3.324276304354.92478801768-0.3724286849060.466575222278-0.3576735931930.137462710050.24904238978-0.2428811095790.248213511692-0.4056161782920.07969965226840.2992340993250.00105313699234-0.01635608207270.254338634958-0.07107394668430.1832742535852.3563111064319.411547617739.9540191494
31.08650011011-0.0552670855421-0.7330514603890.547583518047-0.2481813676920.669379480728-0.0115937924688-0.303200887509-0.05704487680410.2702594702612.7839053013E-5-0.1104602603250.02990145137690.001601653633730.007094853549440.3851842716310.00276232559318-0.03709634821250.393431320762-0.0413078962950.2049841822424.8805974941418.676865470150.6184409599
44.601517216922.69173826289-5.217705847413.92637877756-5.133429977887.6332226351-0.011358510272-0.04624867832360.3143076821040.2853517156960.1421131773250.0438522346402-0.0233955753912-0.200323970971-0.0670456305560.2782595388750.0281529369326-0.04196293476240.217500890767-0.0710943022910.16802513400522.825787902917.782282830738.766321993
51.64334271446-0.8318361550310.5121243392891.41327763814-0.3066039313370.51445060279-0.165390950063-0.08201533833160.4258735550210.1892717987260.071668827361-0.133850598438-0.1868019798210.01508310436840.09396766108940.229467410752-0.04439085734340.01607314190710.152829201505-0.03893779649820.40083101036420.536039810747.97490565165.56964634349
69.09345402039-6.354516817685.627797154464.19949386298-3.771657774053.239119782810.373491235667-0.53222248432-0.404168545463-0.2718170791420.160633606550.5642073519910.287804905045-0.273809969898-0.5297359223310.176049175526-0.0501800252421-0.002728278772010.209476226120.01822023422260.39339884527218.126078564640.2372351126.07424311888
71.02341760464-0.7587842024650.3615930907240.704017442699-0.3237881742130.489028694503-0.0641293691485-0.1440763437770.2171004214330.09251428737530.084715205064-0.0858428674792-0.1262918840010.0209580351732-0.0135382400770.222913598677-0.0458113735019-0.002041635458180.177564987617-0.05603939935810.40368806421318.625375149249.794319366712.1572976099
85.6528601104-6.86301162605-0.3340547505289.07754765289-0.1310169757781.493174234280.02918837226430.02283550026830.3813178230960.0734675216168-0.149457409038-0.196338422770.0493036038976-0.01031831146450.1338373111290.134514865171-0.05083253028540.01639220336890.180113156084-0.02362730922390.26266110392326.747703705832.930933723422.996403513
92.005991736742.079383808073.052029067354.210312238843.202285799832.660122972980.452978946102-0.940153133339-0.937738161952-0.0109417720815-0.457364718772-0.9951370733840.46585723639-0.1930151344420.03888243403860.3024819580070.0223489599177-0.04611065709830.2396490207110.1271949662820.38325179875332.9896213545-39.070899414229.7625549776
101.02242084212-1.364019821440.1768846449794.759467108870.5118567349380.500423096161-0.0312599137933-0.168646151570.02070957432390.0975002414250.103927359474-0.369987837222-0.01173168083480.14131256913-0.02909604013830.240494549993-0.0103521495676-0.05411323283810.2944344861450.04688144876750.22417058285231.7978345779-10.483361679639.5644191731
11-0.0767524620013-0.152488105514-0.1625246397082.043404239342.625455235870.356965757453-0.0606897658735-0.0294150301888-0.016615493577-0.8749743800440.05231055975440.526966145272-0.160523878460.03594979960360.03337337262820.314503910842-0.00621725580856-0.06059021049820.2787376090340.02079023365090.27452619933628.264039733-13.78716027931.5297609701
120.3921448283980.173510400021-0.3255789376181.857450711090.420076135480.1833007052230.0127676321946-0.207866235368-0.09272345795210.1289259857620.0286780380381-0.316308569087-0.008171400070880.155450214354-0.02846801134120.305749390687-0.00982734008721-0.1120779882230.2966313858140.03504290761060.3391150970438.5375548323-16.71517413834.3950493602
135.15553162016-5.33074135198-1.903051084869.267825173690.8502940003231.06265671401-0.0455028657710.0787232149517-0.05010538620320.1967385581620.05160388845710.2082954312940.0399760980126-0.000679205447914-0.02499506447560.172319701806-0.017386710707-0.05884519621940.230408692401-0.007089391020060.13276073795138.10136698314.4024326371229.6568127821
140.7547421862990.0504987941005-0.0005824324317730.3252749812810.03514855343092.96523781199-0.09419365031020.1050518560260.00208975035226-0.0100992467179-0.0629296751629-0.260690690253-0.2390193692970.2164055589710.1302091976460.13422329615-0.02115245870030.00568260377460.1708506697280.02141531241550.45081026049351.6821635957.32205459325-3.64965996508
150.679415071887-0.117517935933-1.887263856260.131715577681.137818619395.15683471235-0.08097988192970.103053168261-0.01477730001730.0149874418614-0.127475541128-0.07975288807520.183603777463-0.3105768690730.1765886264880.1775912322640.03477766164810.005009165336620.1991899083850.0006147499666570.39359502639444.04787292727.22718121828-2.10251522018
160.2102265321350.160398643949-0.4446773206660.447289458996-0.04710679264471.05629515857-0.0194557718804-0.01090074857390.02594519122130.00427184983573-0.00206494433063-0.339175547201-0.1906996887070.1177761293697.36938875677E-50.142197398071-0.01566520456360.005422125685860.248555639193-0.002409974456220.5160968181154.289871506313.2267963955-0.246952640826
174.7892745164-2.077778136250.2854764520844.687830932940.4045100533864.65035705884-0.283131254767-0.06625704181020.2806263275850.1104732914660.1762891129450.2058256223590.121264769614-0.6265409486620.07315386630660.171269162556-0.003986244805520.01719305736630.2272750745940.001098775116580.39144214912546.194285758817.6304822961-16.4384995152
182.264843785651.58109267504-4.773895621132.88313321575-3.243076966892.10537445588-0.0581607088389-0.007710235529250.06370486621210.1154824517560.00381389164426-0.02087189114810.317308977298-0.1381812571220.02595512321620.16627933554-0.00840341395895-0.05540998997030.198259963051-0.00100080548130.36000514931842.214205656419.821514006513.9936417583
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 5 through 48 )
2X-RAY DIFFRACTION2chain 'D' and (resid 49 through 76 )
3X-RAY DIFFRACTION3chain 'D' and (resid 77 through 137 )
4X-RAY DIFFRACTION4chain 'D' and (resid 138 through 176 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 48 )
6X-RAY DIFFRACTION6chain 'B' and (resid 49 through 76 )
7X-RAY DIFFRACTION7chain 'B' and (resid 77 through 137 )
8X-RAY DIFFRACTION8chain 'B' and (resid 138 through 176 )
9X-RAY DIFFRACTION9chain 'C' and (resid 4 through 13 )
10X-RAY DIFFRACTION10chain 'C' and (resid 14 through 48 )
11X-RAY DIFFRACTION11chain 'C' and (resid 49 through 76 )
12X-RAY DIFFRACTION12chain 'C' and (resid 77 through 137 )
13X-RAY DIFFRACTION13chain 'C' and (resid 138 through 176 )
14X-RAY DIFFRACTION14chain 'A' and (resid 4 through 48 )
15X-RAY DIFFRACTION15chain 'A' and (resid 49 through 76 )
16X-RAY DIFFRACTION16chain 'A' and (resid 77 through 123 )
17X-RAY DIFFRACTION17chain 'A' and (resid 124 through 137 )
18X-RAY DIFFRACTION18chain 'A' and (resid 138 through 176 )

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