[English] 日本語
Yorodumi
- PDB-9cq5: Mn-bound RuBisCO from spinach with CABP inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9cq5
TitleMn-bound RuBisCO from spinach with CABP inhibitor
Components
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose bisphosphate carboxylase small subunit, chloroplastic 2
KeywordsPLANT PROTEIN / Carboxylase / Oxygenase / Inhibitor / Manganese / PHOTOSYNTHESIS
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. ...Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain
Similarity search - Domain/homology
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / : / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit, chloroplastic 2
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVoland, R.W. / Lancaster, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE- 1904310 United States
Citation
Journal: J.Inorg.Biochem. / Year: 2024
Title: The structure of Mn(II)-bound Rubisco from Spinacia oleracea.
Authors: Voland, R.W. / Coleman, R.E. / Lancaster, K.M.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: Features and development of Coot.
Authors: P Emsley / B Lohkamp / W G Scott / K Cowtan /
Abstract: Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations ...Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are 'discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.
History
DepositionJul 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain
E: Ribulose bisphosphate carboxylase large chain
F: Ribulose bisphosphate carboxylase large chain
G: Ribulose bisphosphate carboxylase large chain
H: Ribulose bisphosphate carboxylase large chain
I: Ribulose bisphosphate carboxylase small subunit, chloroplastic 2
J: Ribulose bisphosphate carboxylase small subunit, chloroplastic 2
K: Ribulose bisphosphate carboxylase small subunit, chloroplastic 2
L: Ribulose bisphosphate carboxylase small subunit, chloroplastic 2
M: Ribulose bisphosphate carboxylase small subunit, chloroplastic 2
N: Ribulose bisphosphate carboxylase small subunit, chloroplastic 2
O: Ribulose bisphosphate carboxylase small subunit, chloroplastic 2
P: Ribulose bisphosphate carboxylase small subunit, chloroplastic 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)543,19632
Polymers539,90716
Non-polymers3,28816
Water15,565864
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area112970 Å2
ΔGint-536 kcal/mol
Surface area118610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.029, 218.893, 111.840
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
Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


Mass: 52849.742 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: P00875, ribulose-bisphosphate carboxylase
#2: Protein
Ribulose bisphosphate carboxylase small subunit, chloroplastic 2 / RuBisCO small subunit 2


Mass: 14638.671 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q43832
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O13P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 864 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.3 / Details: PEG 3350, lithium acetate, potassium phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.984 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.25→154.47 Å / Num. obs: 252873 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 45.37 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.56 / Rpim(I) all: 0.229 / Rrim(I) all: 0.606 / Χ2: 1.06 / Net I/σ(I): 5.9
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 7.5 % / Rmerge(I) obs: 5.222 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 12416 / CC1/2: 0.332 / Rpim(I) all: 2.045 / Rrim(I) all: 5.61 / Χ2: 0.84 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→99.51 Å / SU ML: 0.3611 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2248
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2424 8950 4.84 %
Rwork0.1965 175898 -
obs0.1987 184848 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.26 Å2
Refinement stepCycle: LAST / Resolution: 2.5→99.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37520 0 176 864 38560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007938680
X-RAY DIFFRACTIONf_angle_d1.041652560
X-RAY DIFFRACTIONf_chiral_restr0.0555576
X-RAY DIFFRACTIONf_plane_restr0.01136816
X-RAY DIFFRACTIONf_dihedral_angle_d7.03215336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.36662960.29945815X-RAY DIFFRACTION99.97
2.53-2.560.3322990.29255774X-RAY DIFFRACTION99.97
2.56-2.590.34932930.29525822X-RAY DIFFRACTION99.93
2.59-2.620.34192920.28095777X-RAY DIFFRACTION100
2.62-2.660.29392960.2715818X-RAY DIFFRACTION99.98
2.66-2.690.35082990.2765822X-RAY DIFFRACTION99.97
2.69-2.730.3243000.27285828X-RAY DIFFRACTION99.98
2.73-2.770.33892910.26215765X-RAY DIFFRACTION99.98
2.77-2.820.3143000.25635851X-RAY DIFFRACTION100
2.82-2.860.30012930.25035837X-RAY DIFFRACTION99.98
2.86-2.910.31672930.26025797X-RAY DIFFRACTION100
2.91-2.960.32312940.25975818X-RAY DIFFRACTION100
2.96-3.020.32622960.25125845X-RAY DIFFRACTION99.97
3.02-3.080.28222970.24135803X-RAY DIFFRACTION100
3.08-3.150.27612980.23575839X-RAY DIFFRACTION100
3.15-3.220.27283000.23225846X-RAY DIFFRACTION99.98
3.22-3.30.26392950.21225823X-RAY DIFFRACTION99.98
3.3-3.390.283020.20455866X-RAY DIFFRACTION100
3.39-3.490.27152950.21095827X-RAY DIFFRACTION99.98
3.49-3.610.24433010.19195883X-RAY DIFFRACTION100
3.61-3.730.24593010.18845855X-RAY DIFFRACTION99.92
3.73-3.880.22142920.17115843X-RAY DIFFRACTION100
3.88-4.060.17723000.15615889X-RAY DIFFRACTION99.98
4.06-4.270.20032980.15555875X-RAY DIFFRACTION99.98
4.27-4.540.19453020.15455904X-RAY DIFFRACTION99.97
4.54-4.890.19213040.14615920X-RAY DIFFRACTION100
4.89-5.390.21043050.16275922X-RAY DIFFRACTION100
5.39-6.160.19983000.16655971X-RAY DIFFRACTION100
6.17-7.770.20363050.17016010X-RAY DIFFRACTION100
7.77-99.510.17843130.16236253X-RAY DIFFRACTION99.7

+
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