[English] 日本語
Yorodumi
- PDB-4gn7: mouse SMP30/GNL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gn7
Titlemouse SMP30/GNL
ComponentsRegucalcin
KeywordsHYDROLASE / beta propeller structure
Function / homology
Function and homology information


gluconolactonase / gluconolactonase activity / L-ascorbic acid biosynthetic process / positive regulation of ATP-dependent activity / enzyme regulator activity / regulation of calcium-mediated signaling / intracellular calcium ion homeostasis / calcium ion binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Regucalcin / Senescence marker protein-30 (SMP-30) / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAizawa, S. / Senda, M. / Harada, A. / Maruyama, N. / Ishida, T. / Aigaki, T. / Ishigami, A. / Senda, T.
CitationJournal: Plos One / Year: 2013
Title: Structural basis of the gamma-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase
Authors: Aizawa, S. / Senda, M. / Harada, A. / Maruyama, N. / Ishida, T. / Aigaki, T. / Ishigami, A. / Senda, T.
History
DepositionAug 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Regucalcin
B: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,21517
Polymers66,8862
Non-polymers1,32915
Water6,720373
1
A: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0598
Polymers33,4431
Non-polymers6167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1559
Polymers33,4431
Non-polymers7138
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.678, 102.678, 147.817
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Regucalcin / SMP30 / GNL / RC / Gluconolactonase / Senescence marker protein 30


Mass: 33442.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smp30 / Plasmid: pET-21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q64374, gluconolactonase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.6M ammonium sulfate, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→76.2 Å / Num. all: 66230 / Num. obs: 66230 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 28.69 Å2
Reflection shellResolution: 1.95→2.06 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GN9

4gn9


Resolution: 1.95→51.339 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8569 / SU ML: 0.18 / σ(F): 1.99 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 3311 5 %Random
Rwork0.1852 ---
all0.1867 66221 --
obs0.1867 66221 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.31 Å2 / Biso mean: 32.1372 Å2 / Biso min: 18.53 Å2
Refinement stepCycle: LAST / Resolution: 1.95→51.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4617 0 67 373 5057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074791
X-RAY DIFFRACTIONf_angle_d1.1696513
X-RAY DIFFRACTIONf_chiral_restr0.087705
X-RAY DIFFRACTIONf_plane_restr0.005840
X-RAY DIFFRACTIONf_dihedral_angle_d13.5261719
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9501-1.97790.27091390.224226362775100
1.9779-2.00740.26041350.214425672702100
2.0074-2.03880.24821350.21525642699100
2.0388-2.07220.25021370.198626132750100
2.0722-2.1080.24981360.202825742710100
2.108-2.14630.24211370.207526112748100
2.1463-2.18760.2481360.20225812717100
2.1876-2.23220.25431360.194725892725100
2.2322-2.28080.2311380.193626212759100
2.2808-2.33380.22181380.201426102748100
2.3338-2.39220.22541360.194125792715100
2.3922-2.45690.25751360.197325862722100
2.4569-2.52920.24791370.200926092746100
2.5292-2.61080.24831370.201126102747100
2.6108-2.70410.25961370.212926002737100
2.7041-2.81240.26261390.216926362775100
2.8124-2.94030.24841380.225226212759100
2.9403-3.09530.28181380.221626272765100
3.0953-3.28930.22491390.196826402779100
3.2893-3.54320.19781380.179626202758100
3.5432-3.89960.1911400.157926542794100
3.8996-4.46360.16611400.143126692809100
4.4636-5.62260.16561420.142827032845100
5.6226-51.35680.1821470.18792790293799

+
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