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

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Basic information

Entry
Database: PDB / ID: 6wyg
TitleCrystal structure of Human H-chain Ferritin variant 157C Delta C-star Modified with a RAFT agent
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 / 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 / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / Chem-RFT / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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

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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)86,56625
Polymers84,2374
Non-polymers2,32921
Water4,846269
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)519,398150
Polymers505,42124
Non-polymers13,977126
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 area96540 Å2
ΔGint-1150 kcal/mol
Surface area137540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.810, 126.810, 281.285
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

31C-360-

HOH

41C-367-

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.: 9 / Source method: isolated from a natural source / Formula: Fe
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: 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: obtained synthetically / Formula: C15H24N2O3S3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 5 uL reservoir + 5 uL 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.27→93.76 Å / Num. obs: 38783 / % possible obs: 95.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 34.69 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.6
Reflection shellResolution: 2.27→2.34 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3707 / CC1/2: 0.843

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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: 2.27→50.07 Å / SU ML: 0.3348 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.266
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.26 3839 10.09 %
Rwork0.1976 34223 -
obs0.2039 38062 93.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.55 Å2
Refinement stepCycle: LAST / Resolution: 2.27→50.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5478 0 49 269 5796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00785632
X-RAY DIFFRACTIONf_angle_d0.90237631
X-RAY DIFFRACTIONf_chiral_restr0.0472816
X-RAY DIFFRACTIONf_plane_restr0.00521019
X-RAY DIFFRACTIONf_dihedral_angle_d10.87759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.30.64321020.6332881X-RAY DIFFRACTION65.71
2.3-2.330.46521210.39471212X-RAY DIFFRACTION90.01
2.33-2.360.34421360.23671342X-RAY DIFFRACTION99.53
2.36-2.40.31981630.24211314X-RAY DIFFRACTION98.86
2.4-2.430.29841550.22981292X-RAY DIFFRACTION97.77
2.43-2.470.30751410.22781320X-RAY DIFFRACTION98.98
2.47-2.510.30711290.21371339X-RAY DIFFRACTION99.73
2.51-2.550.28811530.2061338X-RAY DIFFRACTION99.87
2.55-2.60.32131630.23181318X-RAY DIFFRACTION99.73
2.6-2.650.27041560.22291326X-RAY DIFFRACTION99.26
2.65-2.70.3181990.2283820X-RAY DIFFRACTION61.14
2.7-2.760.28911660.22791307X-RAY DIFFRACTION99.8
2.76-2.830.34751490.25971329X-RAY DIFFRACTION99.39
2.83-2.90.33481570.23871332X-RAY DIFFRACTION99.47
2.9-2.980.26951330.22591300X-RAY DIFFRACTION96.96
2.98-3.060.29751510.21991327X-RAY DIFFRACTION99.19
3.06-3.160.26981430.20061361X-RAY DIFFRACTION100
3.16-3.280.30131640.19781327X-RAY DIFFRACTION99.87
3.28-3.410.26371530.18651346X-RAY DIFFRACTION99.73
3.41-3.560.23851070.17231007X-RAY DIFFRACTION74.92
3.56-3.750.18461240.15961079X-RAY DIFFRACTION79.77
3.75-3.980.24541270.16111112X-RAY DIFFRACTION81.46
3.98-4.290.20771370.14581367X-RAY DIFFRACTION99.8
4.29-4.720.19831520.1341364X-RAY DIFFRACTION100
4.72-5.410.19221490.15381370X-RAY DIFFRACTION99.15
5.41-6.80.2461500.20441351X-RAY DIFFRACTION98.04
6.81-50.070.22431590.18941442X-RAY DIFFRACTION98.16
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)
10.448599272324-0.09938468299610.1898189355180.566486448973-0.08576256417140.615216469667-0.21783567404-0.4321211707550.2563886956970.736084838319-0.118720244955-0.1992759279820.013396831083-0.1588461212070.1140897525470.827778336634-0.03543385556830.04448310156380.784304144288-0.4278644009650.3096987948961.6073937065223.143397487146.1781824039
21.03570226391-0.198622451548-0.1932373238020.307481573316-0.1625706833130.19258378699-0.148119508579-0.6487697655940.2831913781560.6748069776290.0729451334091-0.08011893827450.0529467166470.02433049815850.07307050537430.8786836476350.0150353541984-0.1364661208550.804031347162-0.2309802750930.3516811116786.6914667879817.846355166246.070405088
38.20767214868-0.42580007342-6.115569023714.08064469661-3.868791966838.866949628840.149215943926-0.7387614464940.8966683378090.949487402623-0.29072644405-0.214774750142-0.2067268038560.6297832963880.129725784670.651618525132-0.0385709509024-0.2587804442130.415448575824-0.1866919751640.64086034093427.256546949822.126650448933.0006293342
40.200235982429-0.0307312680421-0.128263617311.2583857307-0.1322213906570.295407439024-0.107531989137-0.1620436051460.7955129335730.01914667421220.0413956487877-0.0142718464938-0.1495944147190.3220933076840.07532142746250.339966197902-0.0568949903483-0.1217274871110.0821844326284-0.03652550115841.0805361940320.734196067746.92743454075.79742939937
59.31644735013-7.126170991655.566096872465.37032592376-4.1948776723.288163377860.573094412614-0.468681865210.0801201762817-0.4479200377040.08345928055890.47735424410.399239358451-0.254664756686-0.6216298168290.342049948548-0.0538158716243-0.07085516961570.2954456204030.0171381879050.86851994910618.453746660439.29149246426.24272941765
60.684803257953-0.414670328677-0.1205349812021.57482718203-0.5504259454220.275051962283-0.133642371626-0.2112010425320.7612729138770.3482808602350.061663930965-0.199568090686-0.1350064596560.005490680411990.03593439575740.395624097742-0.0304628366076-0.1380678382590.34971455528-0.1494955190751.0053736211118.836193785846.432888669114.4136678336
77.65534670573-1.91410611989-5.013148931353.06160116807-3.018494505042.007354346660.0513676666152-0.1893889173090.3577884141120.244957300756-0.0547851861804-0.231518915851-0.5492873501990.777890148242-0.0009708963368090.434027422694-0.0270493438741-0.2485517297630.457536417827-0.08821923588270.8665560744433.035090536327.191483065422.8775094607
80.536585186987-0.157895762127-0.135049004361.339390317770.7222700537910.823439198614-0.0566794403564-0.541876241744-0.3158986913890.237254832717-0.0649137709353-0.415774334357-0.02554234663610.2800614109250.03773061888230.5688346031310.0402047247807-0.4836356768440.539201088320.433825583540.57695182756232.564849322-20.105141389436.3673069631
90.714099003935-0.838646746068-0.2157193518766.08591129943-0.2879892166150.0903887768706-0.146367099351-0.477032771325-0.134664935296-0.1087562597650.1193222249750.0399447744364-0.1014420162160.1290020879440.04869835570090.4804409007190.00189769714647-0.2116470947450.5099239429340.08037216418960.4454623722627.811494406-8.9932261546533.7365530964
100.2380644700060.454376558257-0.105509262441.83724515469-0.2877181942720.1988631706750.040363416882-0.549037791312-0.3203302708430.534395988806-0.000525707330548-0.8313429173560.05183807257840.0341645125106-0.00408519476110.5495195116380.0251745039203-0.3257557609550.6195664400460.1703985099040.74567143870538.7581356012-13.622287365832.2591723023
113.27224355889-0.834385497908-4.048314940487.213981202123.775318883296.07362434034-0.175557066986-0.7844318855780.4294328806210.703282772418-0.386145634832-0.540561904391-0.4006821749380.2175834017070.5303173450390.5603491735830.0140316429283-0.301598378370.491940748464-0.01879575483210.53416272898234.058486460611.590573767931.7867245296
121.398148578280.2497661290640.7470675638940.762646611661-0.4077284296811.40986916601-0.1028204717590.1454944951690.0746577561439-0.0587424148878-0.131430051436-0.609188180255-0.112642273980.2797386802730.266871191010.2643507954930.01300180546110.04103857529790.2618041621310.08991301466980.90888830251451.00940777137.32939156055-3.29566803111
130.097824451952-0.178140491467-0.9442139805480.4542793598140.7439087863132.01049516827-0.03683251423340.1345206488860.408942897274-0.10202878954-0.0184217961431-0.376252672179-0.237826643872-0.6652209479540.08643028828150.2809931575630.0167298214482-0.03180412711430.3728388736190.07691159011530.85043783019243.16936273827.21649745643-1.51109954283
140.836593448696-0.117272048873-0.4194611701220.8853947762350.4421946562411.54431017732-0.02293439231830.0422226664040.240930844416-0.0579604089335-0.0249479808295-0.741112309106-0.2176262826210.1644993201860.02778579658220.319121959184-0.0186171698218-0.01235564160450.3175038806180.09669100080271.001432560449.517495450916.020341954-1.61245381305
152.486971192071.19708388148-3.820582122382.40414748966-0.0977156221627.52179292114-0.104079846732-0.434787211073-0.02921567513950.4599308260390.054752298507-0.780645127133-0.01859771546620.6325093068270.02848147872470.3743385765940.000303513849083-0.251345175680.4227465460430.03752622627310.76667829754139.743949519116.062671809321.6739974119
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 157 )
3X-RAY DIFFRACTION3chain 'D' and (resid 158 through 176 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 48 )
5X-RAY DIFFRACTION5chain 'B' and (resid 49 through 75 )
6X-RAY DIFFRACTION6chain 'B' and (resid 76 through 157 )
7X-RAY DIFFRACTION7chain 'B' and (resid 158 through 176 )
8X-RAY DIFFRACTION8chain 'C' and (resid 5 through 42 )
9X-RAY DIFFRACTION9chain 'C' and (resid 43 through 75 )
10X-RAY DIFFRACTION10chain 'C' and (resid 76 through 157 )
11X-RAY DIFFRACTION11chain 'C' and (resid 158 through 176 )
12X-RAY DIFFRACTION12chain 'A' and (resid 5 through 48 )
13X-RAY DIFFRACTION13chain 'A' and (resid 49 through 75 )
14X-RAY DIFFRACTION14chain 'A' and (resid 76 through 158 )
15X-RAY DIFFRACTION15chain 'A' and (resid 159 through 176 )

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