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- PDB-6ls2: Marsupenaeus japonicus ferritin mutant (T158H) pH 4.0 -

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Basic information

Entry
Database: PDB / ID: 6ls2
TitleMarsupenaeus japonicus ferritin mutant (T158H) pH 4.0
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
Biological speciesPenaeus japonicus (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
B: Ferritin


Theoretical massNumber of molelcules
Total (without water)39,0562
Polymers39,0562
Non-polymers00
Water4,810267
1
A: Ferritin
B: Ferritin
x 12


Theoretical massNumber of molelcules
Total (without water)468,66924
Polymers468,66924
Non-polymers00
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 area89840 Å2
ΔGint-347 kcal/mol
Surface area131260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.435, 117.435, 117.435
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23

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Components

#1: Protein Ferritin


Mass: 19527.873 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 3.46 Å3/Da / Density % sol: 64.41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: 2M NaCl, 100 mM KH2PO3/NaHPO3 pH 4.0

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Data collection

DiffractionMean temperature: 273.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 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: 1.6→50 Å / Num. obs: 71219 / % possible obs: 100 % / Redundancy: 19.1 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.03 / Rrim(I) all: 0.13 / Χ2: 0.755 / Net I/σ(I): 3.6 / Num. measured all: 1357878
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.6-1.6618.61.03170620.8440.2451.060.453
1.66-1.7218.90.82470620.9050.1940.8470.473
1.72-1.818.10.65570580.9260.1580.6740.511
1.8-1.918.80.4970250.950.1160.5030.624
1.9-2.0219.30.37371110.9730.0870.3830.796
2.02-2.1718.40.27870930.9840.0660.2861.06
2.17-2.3919.40.1771070.9930.0390.1740.904
2.39-2.7419.60.12771590.9960.0290.1310.921
2.74-3.4520.20.08871550.9980.020.0910.982
3.45-5019.30.0673870.9990.0140.0620.778

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4U

6a4u


Resolution: 1.6→23.5 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.198 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.065
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1896 3397 4.8 %RANDOM
Rwork0.1702 ---
obs0.1711 67759 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.83 Å2 / Biso mean: 19.296 Å2 / Biso min: 10.22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.6→23.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 0 267 2991
Biso mean---26.91 -
Num. residues----338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0142774
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172438
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.6533732
X-RAY DIFFRACTIONr_angle_other_deg1.1641.6425738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9915336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36624.444162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97715512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7871512
X-RAY DIFFRACTIONr_chiral_restr0.0810.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02504
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 228 -
Rwork0.219 5002 -
all-5230 -
obs--100 %

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