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- PDB-6lrw: Marsupenaeus japonicus ferritin mutant(T158H) pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 6lrw
TitleMarsupenaeus japonicus ferritin mutant(T158H) pH 7.0
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: 2.4 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 China
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 1.0Dec 23, 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
Water1,69394
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 area91070 Å2
ΔGint-266 kcal/mol
Surface area132290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.114, 117.114, 117.114
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.: 94 / 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: 3.43 Å3/Da / Density % sol: 64.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 2500 mM NaCl, 100 mM KH2PO3 / KH2PO3 (pH 7.0)

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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: 2.4→117.11 Å / Num. obs: 21207 / % possible obs: 100 % / Redundancy: 19.1 % / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.033 / Rrim(I) all: 0.146 / Χ2: 0.554 / Net I/σ(I): 3.9
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.4-2.4417.50.48210440.9650.1180.4970.457
2.44-2.4917.70.48110580.970.1170.4950.457
2.49-2.5317.90.43910180.9720.1060.4520.465
2.53-2.5918.90.37510770.9770.0880.3850.455
2.59-2.6419.50.34310340.980.0790.3520.466
2.64-2.719.40.33110430.9820.0770.340.51
2.7-2.7719.40.30110440.9880.070.3090.471
2.77-2.8519.30.25810570.9910.060.2650.482
2.85-2.9319.30.21610550.9930.050.2220.503
2.93-3.0219.40.19310400.9940.0450.1990.52
3.02-3.1318.60.17410580.9950.0410.1790.537
3.13-3.2618.30.14810550.9960.0350.1520.564
3.26-3.4119.50.13610470.9970.0320.140.592
3.41-3.5820.70.1210790.9970.0270.1230.667
3.58-3.8120.60.10410530.9980.0230.1070.706
3.81-4.120.30.09110560.9980.0210.0940.712
4.1-4.5219.10.08410870.9980.020.0860.743
4.52-5.1718.60.07510720.9990.0180.0770.66
5.17-6.5120.30.09410870.9980.0210.0960.545
6.51-50180.054114310.0130.0560.503

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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: 2.4→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.233 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.209
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1118 5.3 %RANDOM
Rwork0.1757 ---
obs0.1785 20089 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 76.35 Å2 / Biso mean: 23.269 Å2 / Biso min: 4.61 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 0 94 2818
Biso mean---17.5 -
Num. residues----338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192774
X-RAY DIFFRACTIONr_bond_other_d0.0020.022586
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.9583730
X-RAY DIFFRACTIONr_angle_other_deg1.00935970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4575336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.74525.6150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.38315512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2721512
X-RAY DIFFRACTIONr_chiral_restr0.1010.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023192
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02640
LS refinement shellResolution: 2.402→2.464 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 74 -
Rwork0.214 1471 -
all-1545 -
obs--100 %

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