[English] 日本語
Yorodumi
- PDB-7b2o: Crystal structure of Chlamydomonas reinhardtii chloroplastic sedo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7b2o
TitleCrystal structure of Chlamydomonas reinhardtii chloroplastic sedoheptulose-1,7-bisphosphatase
ComponentsFBPase domain-containing protein
KeywordsPHOTOSYNTHESIS / sedoheptulose-1 / 7-bisphosphatase / SBPase / Chlamydomonas reinhardtii / 7-bisphosphate / sedoheptulose-7-phosphate / Calvin-benson cycle
Function / homology
Function and homology information


sedoheptulose-bisphosphatase activity / starch biosynthetic process / thylakoid / sucrose biosynthetic process / apoplast / fructose 1,6-bisphosphate 1-phosphatase activity / chloroplast envelope / fructose 6-phosphate metabolic process / fructose metabolic process / fructose 1,6-bisphosphate metabolic process ...sedoheptulose-bisphosphatase activity / starch biosynthetic process / thylakoid / sucrose biosynthetic process / apoplast / fructose 1,6-bisphosphate 1-phosphatase activity / chloroplast envelope / fructose 6-phosphate metabolic process / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / chloroplast stroma / gluconeogenesis / defense response to bacterium / metal ion binding / cytoplasm
Similarity search - Function
Sedoheptulose-1,7-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsLe Moigne, T. / Lemaire, S.D. / Henri, J.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)JCJC CALVINTERACT ANR-19-CE11-0009 France
CitationJournal: To Be Published
Title: Crystal structure of Chlamydomonas reinhardtii chloroplastic sedoheptulose-1,7-bisphosphatas
Authors: Le Moigne, T. / Lemaire, S.D. / Henri, J.
History
DepositionNov 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: FBPase domain-containing protein
B: FBPase domain-containing protein
C: FBPase domain-containing protein
D: FBPase domain-containing protein
E: FBPase domain-containing protein
F: FBPase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)217,3246
Polymers217,3246
Non-polymers00
Water724
1
A: FBPase domain-containing protein
F: FBPase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)72,4412
Polymers72,4412
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-16 kcal/mol
Surface area22480 Å2
MethodPISA
2
B: FBPase domain-containing protein
E: FBPase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)72,4412
Polymers72,4412
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-16 kcal/mol
Surface area21990 Å2
MethodPISA
3
C: FBPase domain-containing protein
D: FBPase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)72,4412
Polymers72,4412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-17 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.224, 183.652, 75.196
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

#1: Protein
FBPase domain-containing protein / Sedoheptulose-1 / 7-bisphosphatase / chloroplastic


Mass: 36220.684 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_03g185550v5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2K3DY10, sedoheptulose-bisphosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.83 Å3/Da / Density % sol: 56.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium HEPES pH 7.5; 2% (v/v) PEG 400; 2.0 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980113458075 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980113458075 Å / Relative weight: 1
ReflectionResolution: 3.09→47.47 Å / Num. obs: 45740 / % possible obs: 99.34 % / Redundancy: 13.4 % / Biso Wilson estimate: 64.82 Å2 / CC1/2: 0.983 / CC star: 0.996 / Net I/σ(I): 12.02
Reflection shellResolution: 3.09→3.2 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 1.72 / Num. unique obs: 4245 / CC1/2: 0.623 / CC star: 0.876 / % possible all: 94.2

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IZ3

5iz3


Resolution: 3.09→47.47 Å / SU ML: 0.4227 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5258
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2383 1986 4.35 %
Rwork0.1933 43622 -
obs0.1953 45608 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67 Å2
Refinement stepCycle: LAST / Resolution: 3.09→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14172 0 0 4 14176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004614486
X-RAY DIFFRACTIONf_angle_d0.737419605
X-RAY DIFFRACTIONf_chiral_restr0.04882206
X-RAY DIFFRACTIONf_plane_restr0.00522539
X-RAY DIFFRACTIONf_dihedral_angle_d5.98711989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.170.36231350.31892844X-RAY DIFFRACTION92
3.17-3.260.31171350.28143073X-RAY DIFFRACTION99.94
3.26-3.350.34351360.26943066X-RAY DIFFRACTION99.91
3.35-3.460.32551440.26173126X-RAY DIFFRACTION99.97
3.46-3.590.30461430.2383099X-RAY DIFFRACTION99.97
3.59-3.730.26921490.21623074X-RAY DIFFRACTION100
3.73-3.90.25371320.19683106X-RAY DIFFRACTION100
3.9-4.10.24051490.19173111X-RAY DIFFRACTION99.97
4.1-4.360.21011430.16623118X-RAY DIFFRACTION100
4.36-4.70.1861430.14343150X-RAY DIFFRACTION99.97
4.7-5.170.19791430.15583120X-RAY DIFFRACTION100
5.17-5.920.2081340.16663181X-RAY DIFFRACTION100
5.92-7.450.21671510.18653211X-RAY DIFFRACTION100
7.45-47.470.20031490.17163343X-RAY DIFFRACTION99.63

+
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