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- PDB-5v5k: Crystal structure of ferritin E65R mutant from hyperthermophilic ... -

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Basic information

Entry
Database: PDB / ID: 5v5k
TitleCrystal structure of ferritin E65R mutant from hyperthermophilic archaeon Archaeoglobus fulgidus
ComponentsFerritin
KeywordsOXIDOREDUCTASE / Ferritin / cage / ferroxidase / self-assembly
Function / homology
Function and homology information


ferric iron binding / iron ion transport / intracellular iron ion homeostasis / identical protein binding
Similarity search - Function
Ferritin, prokaryotic-type / 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 ...Ferritin, prokaryotic-type / 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 speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.08 Å
AuthorsRoose, B.W. / Pulsipher, K.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)PD 09-6885 United States
CitationJournal: Biochemistry / Year: 2017
Title: Thermophilic Ferritin 24mer Assembly and Nanoparticle Encapsulation Modulated by Interdimer Electrostatic Repulsion.
Authors: Pulsipher, K.W. / Villegas, J.A. / Roose, B.W. / Hicks, T.L. / Yoon, J. / Saven, J.G. / Dmochowski, I.J.
History
DepositionMar 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin


Theoretical massNumber of molelcules
Total (without water)153,0708
Polymers153,0708
Non-polymers00
Water0
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin


Theoretical massNumber of molelcules
Total (without water)459,21124
Polymers459,21124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Unit cell
Length a, b, c (Å)171.730, 171.730, 171.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 3 - 164 / Label seq-ID: 1 - 162

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD
5chain EEE
6chain FFF
7chain GGG
8chain HHH

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Components

#1: Protein
Ferritin /


Mass: 19133.781 Da / Num. of mol.: 8 / Mutation: E65R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: pJ414 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RP / References: UniProt: O29424

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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: 2.76 Å3/Da / Density % sol: 55.39 % / Description: octahedral
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.45 M potassium phosphate monobasic, 0.3 M sodium phosphate monobasic, 5% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.49
ReflectionResolution: 3.08→99.15 Å / Num. obs: 31499 / % possible obs: 100 % / Redundancy: 18 % / CC1/2: 0.999 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.04 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
3.08-3.2518.91.0560.571100
9.74-99.1516.90.0541199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S3Q

1s3q


Resolution: 3.08→99.148 Å / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 27.85
RfactorNum. reflection% reflection
Rfree0.2705 3056 5.05 %
Rwork0.2592 --
obs0.2646 31459 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.89 Å2 / Biso mean: 50.4977 Å2 / Biso min: 11.3 Å2
Refinement stepCycle: final / Resolution: 3.08→99.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6440 0 0 0 6440
Num. residues----1296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096432
X-RAY DIFFRACTIONf_angle_d1.0658968
X-RAY DIFFRACTIONf_chiral_restr0.0421256
X-RAY DIFFRACTIONf_plane_restr0.0031288
X-RAY DIFFRACTIONf_dihedral_angle_d3.2731288
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3864X-RAY DIFFRACTION6.526TORSIONAL
12B3864X-RAY DIFFRACTION6.526TORSIONAL
13C3864X-RAY DIFFRACTION6.526TORSIONAL
14D3864X-RAY DIFFRACTION6.526TORSIONAL
15E3864X-RAY DIFFRACTION6.526TORSIONAL
16F3864X-RAY DIFFRACTION6.526TORSIONAL
17G3864X-RAY DIFFRACTION6.526TORSIONAL
18H3864X-RAY DIFFRACTION6.526TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0839-3.1370.37741580.32232899305795
3.137-3.1940.30381300.30752893302396
3.194-3.25540.31481380.29672877301595
3.2554-3.32180.29771760.30152852302894
3.3218-3.3940.33521000.28692915301597
3.394-3.47280.32651580.29372822298095
3.4728-3.55960.32191640.2792884304895
3.5596-3.65570.27891780.27762816299494
3.6557-3.76320.31761620.2772842300495
3.7632-3.88450.27441720.26472823299594
3.8845-4.02310.21941240.25592892301696
4.0231-4.18390.27621440.2482936308095
4.1839-4.3740.24851720.25082783295594
4.374-4.60410.231840.23672832301694
4.6041-4.89180.22351480.26572885303395
4.8918-5.26830.26651550.26922841299695
5.2683-5.79610.29351260.27692899302596
5.7961-6.62960.38211200.28862896301696
6.6296-8.33290.23221880.24142840302894
8.3329-34.34810.25791590.22332850300995

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