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- PDB-6lrv: Marsupenaeus japonicus ferritin mutant(T158H) pH9.0 -

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Basic information

Entry
Database: PDB / ID: 6lrv
TitleMarsupenaeus japonicus ferritin mutant(T158H) pH9.0
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / ferroxidase / iron
Function / homology
Function and homology information


ferroxidase / : / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasm
Similarity search - Function
Ferritin / Ferritin, core subunit, four-helix bundle / 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: 2.3 Å
AuthorsZhao, G. / Tan, X. / Zhang, T.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31730069 China
National Natural Science Foundation of China (NSFC)31972018
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
Water1,71195
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 area90130 Å2
ΔGint-328 kcal/mol
Surface area134560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.922, 117.922, 117.922
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.: 95 / 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: 3.5 Å3/Da / Density % sol: 64.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 2500 mM NaCl, 100 mM KH2PO3 / KH2PO3 (pH 8.0)

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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: Jan 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.3→117.92 Å / Num. obs: 24518 / % possible obs: 100 % / Redundancy: 19.7 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.025 / Rrim(I) all: 0.109 / Χ2: 1.588 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.3-2.3419.90.28312010.9820.0650.290.925
2.34-2.3819.70.25512070.9890.0590.2621.018
2.38-2.43190.23712100.9830.0560.2431.126
2.43-2.4818.60.24111940.9860.0570.2481.112
2.48-2.53190.22312280.9880.0530.2291.242
2.53-2.5920.30.20412240.9880.0460.2091.248
2.59-2.6620.60.19212190.990.0430.1971.393
2.66-2.7320.50.19311970.9920.0440.1981.558
2.73-2.8120.40.17212400.9920.0390.1771.503
2.81-2.920.30.15211860.9940.0350.1561.696
2.9-320.10.14412190.9940.0330.1481.82
3-3.1219.20.13512320.9950.0320.1392.02
3.12-3.2618.50.12612270.9960.030.1292.234
3.26-3.4419.80.11912100.9960.0280.1232.306
3.44-3.6520.70.10612350.9970.0240.1092.337
3.65-3.9320.30.09712410.9970.0220.12.524
3.93-4.3319.90.08412150.9980.0190.0862.165
4.33-4.9518.20.07212580.9980.0170.0741.74
4.95-6.2420.40.06212530.9990.0140.0641.052
6.24-5018.20.041132210.010.0420.676

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6a4u

6a4u


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.798 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.175
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 1299 5.3 %RANDOM
Rwork0.1876 ---
obs0.1892 23219 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 96.53 Å2 / Biso mean: 27.591 Å2 / Biso min: 13.24 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 0 95 2819
Biso mean---25.03 -
Num. residues----338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192774
X-RAY DIFFRACTIONr_bond_other_d0.0020.022586
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.9583730
X-RAY DIFFRACTIONr_angle_other_deg0.98735970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6875336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.43525.6150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50515512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0471512
X-RAY DIFFRACTIONr_chiral_restr0.0990.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023192
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02640
LS refinement shellResolution: 2.302→2.362 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 102 -
Rwork0.177 1694 -
all-1796 -
obs--100 %

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