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- PDB-6j4m: Thermal treated soybean seed H-2 ferritin -

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Basic information

Entry
Database: PDB / ID: 6j4m
TitleThermal treated soybean seed H-2 ferritin
ComponentsFerritin
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / chloroplast / iron ion transport / ferrous iron binding / response to oxidative stress / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
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 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 / Ferritin-2, chloroplastic
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.598 Å
AuthorsZhang, X. / Zang, J. / Chen, H. / Zhou, K. / Zhao, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31730069 China
CitationJournal: Rsc Adv / Year: 2019
Title: Thermostability of protein nanocages: the effect of natural extra peptide on the exterior surface.
Authors: Zhang, X. / Zang, J. / Chen, H. / Zhou, K. / Zhang, T. / Lv, C. / Zhao, G.
History
DepositionJan 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...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 / 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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Ferritin
A: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9029
Polymers47,7312
Non-polymers1707
Water1,45981
1
H: Ferritin
A: Ferritin
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)574,818108
Polymers572,77724
Non-polymers2,04284
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
Buried area100980 Å2
ΔGint-789 kcal/mol
Surface area127260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.902, 149.902, 149.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11H-301-

MG

21A-301-

MG

31H-424-

HOH

41H-431-

HOH

51H-440-

HOH

61A-416-

HOH

71A-440-

HOH

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Components

#1: Protein Ferritin


Mass: 23865.697 Da / Num. of mol.: 2 / Fragment: UNP residues 49-257 / Mutation: E155D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Production host: Escherichia coli (E. coli)
References: UniProt: I1J7H3, UniProt: Q94IC4*PLUS, ferroxidase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 293 K / Method: evaporation / Details: Magnesium chloride, Tris, 1,6-hexylene glycol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.598→40.06 Å / Num. obs: 17380 / % possible obs: 100 % / Redundancy: 11.5 % / CC1/2: 0.99 / Net I/σ(I): 4.5
Reflection shellResolution: 2.598→2.691 Å / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A68

3a68


Resolution: 2.598→40.06 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 21.4
RfactorNum. reflection% reflection
Rfree0.2238 841 4.84 %
Rwork0.1935 --
obs0.195 17380 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.598→40.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 7 81 2780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082748
X-RAY DIFFRACTIONf_angle_d0.953710
X-RAY DIFFRACTIONf_dihedral_angle_d19.8811644
X-RAY DIFFRACTIONf_chiral_restr0.05400
X-RAY DIFFRACTIONf_plane_restr0.005484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5985-2.76120.25161760.18272694X-RAY DIFFRACTION100
2.7612-2.97440.19741460.15622707X-RAY DIFFRACTION100
2.9744-3.27370.19031360.16562751X-RAY DIFFRACTION100
3.2737-3.74720.25691370.16882750X-RAY DIFFRACTION100
3.7472-4.72040.20511360.19092774X-RAY DIFFRACTION100
4.7204-47.4110.24131100.23642865X-RAY DIFFRACTION99

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