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- PDB-7emk: Dendrorhynchus zhejiangensis ferritin -

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Basic information

Entry
Database: PDB / ID: 7emk
TitleDendrorhynchus zhejiangensis ferritin
ComponentsDendrorhynchus zhejiangensis ferritin
KeywordsSTRUCTURAL PROTEIN / Dendrorhynchus zhejiangensis / Ferritin
Function / homology: / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesDendrorhynchus sinensis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsHuan, H.S. / Ming, T.H. / Su, X.R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)41676159 China
CitationJournal: Biochemical and Biophysical Research Communications
Year: 2020
Title: Structure determination of ferritin from Dendrorhynchus zhejiangensis
Authors: Huan, H.S. / Jiang, Q.Q. / Wu, Y. / Qiu, X.T. / Lu, C.Y. / Su, C. / Zhou, J. / Li, Y. / Ming, T.H. / Su, X.R.
History
DepositionApr 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2May 29, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Dendrorhynchus zhejiangensis ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,21048
Polymers19,5221
Non-polymers1,68847
Water1,27971
1
A: Dendrorhynchus zhejiangensis ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)509,0451152
Polymers468,52824
Non-polymers40,5171128
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 area95340 Å2
ΔGint-823 kcal/mol
Surface area137580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.790, 151.790, 151.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-205-

FE

21A-206-

FE

31A-207-

FE

41A-208-

FE

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dendrorhynchus zhejiangensis ferritin


Mass: 19521.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendrorhynchus sinensis (invertebrata) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 118 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.73 Å3/Da / Density % sol: 67.04 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 7.5
Details: 0.2 M calcium chloride dihydrate, 0.1 M HEPES sodium, pH 7.5, and 28% (v/v) polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.96003 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96003 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 13520 / % possible obs: 100 % / Redundancy: 38 % / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.025 / Rrim(I) all: 0.155 / Χ2: 1.124 / Net I/σ(I): 7.2 / Num. measured all: 513539
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3437.40.7876610.9840.130.7970.524100
2.34-2.3836.80.8126610.9880.1380.8240.722100
2.38-2.4335.30.6556550.990.110.6650.53100
2.43-2.4833.40.556540.9920.0940.5580.54799.5
2.48-2.5339.80.4936710.9930.0780.4990.531100
2.53-2.5940.80.4526580.9940.0710.4580.58100
2.59-2.6640.80.3956550.9950.0620.40.572100
2.66-2.7340.60.3336630.9960.0530.3370.637100
2.73-2.8140.10.296720.9970.0460.2930.636100
2.81-2.939.80.2426700.9970.0390.2460.712100
2.9-339.50.26650.9980.0320.2020.775100
3-3.12390.176670.9980.0270.1720.915100
3.12-3.2637.90.1446720.9980.0240.1461.026100
3.26-3.4436.70.1226780.9990.020.1241.3100
3.44-3.6532.70.0996730.9990.0170.11.628100
3.65-3.9340.70.0916810.9990.0140.0921.711100
3.93-4.3340.30.086930.9990.0130.0811.923100
4.33-4.9539.20.0816880.9990.0130.0832.206100
4.95-6.2436.70.0847140.9990.0140.0852.288100
6.24-5032.70.0697690.9990.0120.072.6100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→48 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.863 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1883 684 5.1 %RANDOM
Rwork0.1517 ---
obs0.1536 12829 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.3 Å2 / Biso mean: 30.451 Å2 / Biso min: 18.47 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.3→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1358 0 53 71 1482
Biso mean--64.74 33.05 -
Num. residues----168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0141391
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171210
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.651866
X-RAY DIFFRACTIONr_angle_other_deg1.0311.6542845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2445167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42923.41285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67515251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.238158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021578
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02262
LS refinement shellResolution: 2.305→2.364 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 46 -
Rwork0.18 922 -
all-968 -
obs--100 %

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