[English] 日本語
Yorodumi
- PDB-1iv7: Crystal Structure of Single Chain Monellin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1iv7
TitleCrystal Structure of Single Chain Monellin
ComponentsMonellin
KeywordsPLANT PROTEIN / ALPHA+BETA
Function / homology
Function and homology information


Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / Monellin / Monellin / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Monellin chain A / Monellin chain B
Similarity search - Component
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsTamada, T. / Kato, Y. / Kuroki, R.
CitationJournal: To be Published
Title: The Effect of Single Chain Derivatization on the Structure and Stability of the Monellin
Authors: Kato, Y. / Tamada, T. / Sone, H. / Iijima, H. / Kuroki, R.
History
DepositionMar 15, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Monellin
B: Monellin


Theoretical massNumber of molelcules
Total (without water)22,5762
Polymers22,5762
Non-polymers00
Water1,910106
1
A: Monellin


Theoretical massNumber of molelcules
Total (without water)11,2881
Polymers11,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monellin


Theoretical massNumber of molelcules
Total (without water)11,2881
Polymers11,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.650, 36.260, 46.380
Angle α, β, γ (deg.)90.00, 91.10, 90.00
Int Tables number3
Space group name H-MP121

-
Components

#1: Protein Monellin /


Mass: 11287.853 Da / Num. of mol.: 2 / Mutation: E49N, N50E, E149N, N150E
Source method: isolated from a genetically manipulated source
Details: fusion protein concerning chain A comprise residues 1-50 (MONELLIN, CHAIN B) and 52-96 (MONELLIN, CHAIN A), Including glysine linker. fusion protein concerning chain B comprise residues 101- ...Details: fusion protein concerning chain A comprise residues 1-50 (MONELLIN, CHAIN B) and 52-96 (MONELLIN, CHAIN A), Including glysine linker. fusion protein concerning chain B comprise residues 101-150 (MONELLIN, CHAIN B) and 152-196 (MONELLIN, CHAIN A), Including glysine linker.
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Plasmid: pST6311 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110 / References: UniProt: P02882, UniProt: P02881
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 7.2
Details: PEG8000, potassium phosphate, pH 7.2, micro batch, temperature 277K

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200H / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 19, 1998
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→60 Å / Num. all: 18113 / Num. obs: 17026 / % possible obs: 94 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.067

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
REFMAC5refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MOL

1mol


Resolution: 1.82→15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.762 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24084 870 5.1 %RANDOM
Rwork0.19983 ---
obs0.20202 16119 93.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.272 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20.54 Å2
2--0.35 Å2-
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.82→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 0 106 1702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221636
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2321.9672200
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9553190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.05615314
X-RAY DIFFRACTIONr_chiral_restr0.1540.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021278
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2670.3613
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.5164
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.331
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.4931.5954
X-RAY DIFFRACTIONr_mcangle_it2.67521540
X-RAY DIFFRACTIONr_scbond_it4.6253682
X-RAY DIFFRACTIONr_scangle_it7.4144.5660
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.824→1.871 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.363 59
Rwork0.349 1044

+
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