[English] 日本語
Yorodumi
- PDB-7emk: Dendrorhynchus zhejiangensis ferritin -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more