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

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Basic information

Entry
Database: PDB / ID: 6lru
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 / 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
: / IMIDAZOLE / NICKEL (II) ION / Ferritin
Similarity search - Component
Biological speciesPenaeus japonicus (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZhao, G. / Tan, X. / Zhang, T.
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)19,8396
Polymers19,5281
Non-polymers3115
Water3,423190
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)476,143144
Polymers468,66924
Non-polymers7,474120
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 area103930 Å2
ΔGint-773 kcal/mol
Surface area131980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.349, 117.349, 117.349
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-326-

HOH

31A-418-

HOH

41A-469-

HOH

51A-479-

HOH

61A-490-

HOH

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Components

#1: Protein Ferritin


Mass: 19527.873 Da / Num. of mol.: 1 / Mutation: T157H
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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-FE / FE (III) ION


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


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


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.45 Å3/Da / Density % sol: 64.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 2000 mM NaCl, 100 mM imidazole (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: BL17U1 / Wavelength: 1.4813 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4813 Å / Relative weight: 1
ReflectionResolution: 2.398→50 Å / Num. obs: 20515 / % possible obs: 100 % / Redundancy: 34.3 % / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.042 / Rrim(I) all: 0.241 / Χ2: 1.053 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4937.50.72211090.9950.1190.7320.735100
2.49-2.5935.80.6911020.9940.1170.71.013100
2.59-2.733.30.67511070.9680.1260.6871.315100
2.7-2.8537.10.36311100.9960.060.3690.996100
2.85-3.02370.24511240.9980.0410.2480.998100
3.02-3.2637.40.21611250.9980.0360.2190.964100
3.26-3.5832.10.18511250.9950.0340.1891.124100
3.58-4.128.70.14611430.9930.0290.1491.3399.9
4.1-5.1734.30.10111710.9990.0170.1031.04100
5.17-5030.80.09912770.9990.0180.11.11899.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4U

6a4u


Resolution: 2.4→37.109 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.86
RfactorNum. reflection% reflection
Rfree0.1834 2056 10.02 %
Rwork0.1305 --
obs0.1358 20515 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.4 Å2 / Biso mean: 19.1927 Å2 / Biso min: 5.54 Å2
Refinement stepCycle: final / Resolution: 2.4→37.109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1362 0 21 190 1573
Biso mean--39.26 25.38 -
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
2.4-2.45420.181350.10311238
2.4542-2.51550.17851410.11271246
2.5155-2.58350.16351400.11331214
2.5835-2.65950.20731380.11281227
2.6595-2.74530.19731370.12541217
2.7453-2.84340.16241340.12481240
2.8434-2.95720.17671310.12341223
2.9572-3.09170.20581430.131254
3.0917-3.25470.21961340.12791220
3.2547-3.45840.1871380.15281230
3.4584-3.72520.19191270.14521215
3.7252-4.09970.21351370.12571232
4.0997-4.69190.13391410.11231240
4.6919-5.90750.14941410.13561220
5.9075-37.1090.20061390.1751243

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