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- PDB-6lbd: shrimp ferritin T158R G159R -

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Basic information

Entry
Database: PDB / ID: 6lbd
Titleshrimp ferritin T158R G159R
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / ferroxidase / iron / ferritin
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
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
Biological speciesPenaeus japonicus (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.386 Å
AuthorsZhao, G. / Chen, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31730069 China
National Natural Science Foundation of China31671805 China
CitationJournal: Food Chem / Year: 2021
Title: Construction of thermally robust and porous shrimp ferritin crystalline for molecular encapsulation through intermolecular arginine-arginine attractions.
Authors: Chen, H. / Zhang, T. / Tan, X. / Wang, Y. / Liu, Y. / Zhao, G.
History
DepositionNov 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,05712
Polymers19,6471
Non-polymers41011
Water5,224290
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)481,378288
Polymers471,52924
Non-polymers9,849264
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 area126510 Å2
ΔGint-2966 kcal/mol
Surface area130600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.781, 118.781, 118.781
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-372-

HOH

21A-431-

HOH

31A-492-

HOH

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Components

#1: Protein Ferritin


Mass: 19647.062 Da / Num. of mol.: 1 / Mutation: T158R, G159R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus japonicus (crustacean) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: T2B7E1, ferroxidase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.55 Å3/Da / Density % sol: 65.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M Bis-Tris pH 5.5-6.5, 2.0-3.0 M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 58415 / % possible obs: 82.7 % / Redundancy: 37.6 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.02 / Rrim(I) all: 0.126 / Χ2: 0.628 / Net I/σ(I): 3.1 / Num. measured all: 2197255
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.35-1.430.91.11816790.8590.2011.1360.42224.3
1.4-1.4637.90.91869400.9480.1510.9310.436100
1.46-1.5437.70.61169930.9690.10.6190.48100
1.54-1.64370.47869650.9790.0790.4850.553100
1.64-1.7638.70.37570070.9840.0610.380.655100
1.76-1.94370.27270420.9910.0450.2760.835100
1.94-2.2239.10.18970850.9960.030.1911.206100
2.22-2.838.50.07971730.9990.0130.080.486100
2.8-5036.70.045753110.0070.0450.401100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6a4u

6a4u


Resolution: 1.386→23.756 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 12.74
RfactorNum. reflection% reflection
Rfree0.148 2000 3.43 %
Rwork0.138 --
obs0.1384 58389 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.62 Å2 / Biso mean: 15.6339 Å2 / Biso min: 7.19 Å2
Refinement stepCycle: final / Resolution: 1.386→23.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 11 290 1671
Biso mean--27.39 31.99 -
Num. residues----169
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.3863-1.4210.23621390.20653927
1.421-1.45940.21841420.17453977
1.4594-1.50240.19211400.15563957
1.5024-1.55080.14421390.14983936
1.5508-1.60630.1441420.14063991
1.6063-1.67060.16821410.13893973
1.6706-1.74660.14451410.13873980
1.7466-1.83860.15061410.13513991
1.8386-1.95380.14821430.13844026
1.9538-2.10450.13891420.12894010
2.1045-2.31610.12881430.11824028
2.3161-2.65090.10461450.12714090
2.6509-3.33840.14711470.12954130
3.3384-23.7560.1611550.14584373

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