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- PDB-6lrx: Marsupenaeus japonicus ferritin mutant(T158H) -

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Basic information

Entry
Database: PDB / ID: 6lrx
TitleMarsupenaeus japonicus ferritin mutant(T158H)
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / ferroxidase / iron
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis
Similarity search - Function
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
: / NICKEL (II) ION / Ferritin
Similarity search - Component
Biological speciesPenaeus japonicus (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsZhao, G. / Tan, X.
Funding support1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)
CitationJournal: Commun Chem / Year: 2020
Title: Converting histidine-induced 3D protein arrays in crystals into their 3D analogues in solution by metal coordination cross-linking.
Authors: Tan, X. / Chen, H. / Gu, C. / Zhang, J. / Zhang, T. / Wang, H. / Zhao, G.
History
DepositionJan 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7014
Polymers19,5281
Non-polymers1733
Water5,044280
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)472,82696
Polymers468,66924
Non-polymers4,15872
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 area96890 Å2
ΔGint-843 kcal/mol
Surface area129700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.186, 117.186, 117.186
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-203-

NI

21A-485-

HOH

31A-505-

HOH

41A-514-

HOH

51A-535-

HOH

61A-580-

HOH

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Components

#1: Protein Ferritin /


Mass: 19527.873 Da / Num. of mol.: 1 / Mutation: T158H
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-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 3.43 Å3/Da / Density % sol: 64.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 2500 mM NaCl, 100 mM KH2PO3 / KH2PO3 (pH 8.0), 2 mM NiSO4

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Data collection

DiffractionMean temperature: 273.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 30779 / % possible obs: 100 % / Redundancy: 36.1 % / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.033 / Rrim(I) all: 0.199 / Χ2: 0.615 / Net I/σ(I): 2.9 / Num. measured all: 1110087
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.7-1.7629.61.5930010.8510.2941.6180.426
1.76-1.8332.41.30629970.9070.231.3270.437
1.83-1.9136.51.08530130.9620.181.10.462
1.91-2.02380.72930350.9750.1190.7390.499
2.02-2.14370.4830300.9850.080.4860.547
2.14-2.3136.60.32330420.9920.0540.3270.604
2.31-2.5439.20.23930780.9960.0390.2420.634
2.54-2.9137.10.16830920.9960.0280.170.714
2.91-3.6639.20.1131420.9980.0180.1110.891
3.66-5034.90.06933490.9990.0120.070.836

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4U

6a4u


Resolution: 1.702→27.621 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 14.79
RfactorNum. reflection% reflection
Rfree0.1744 2000 6.5 %
Rwork0.1478 --
obs0.1495 30762 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.95 Å2 / Biso mean: 21.8744 Å2 / Biso min: 10.72 Å2
Refinement stepCycle: final / Resolution: 1.702→27.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1358 0 3 280 1641
Biso mean--23.01 37.34 -
Num. residues----169

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