[English] 日本語
Yorodumi
- PDB-7qsw: L8S8-complex forming RubisCO derived from ancestral sequence reco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qsw
TitleL8S8-complex forming RubisCO derived from ancestral sequence reconstruction of the last common ancestor of SSU-bearing Form I RubisCOs
Components
  • RubisCO large subunit
  • RubisCO small subunit
KeywordsLYASE / Ribulose 1 / 5-bisphosphate carboxylase/oxydase / RubisCO
Function / homology2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZarzycki, J. / Schulz, L. / Erb, T.J. / Hochberg, G.K.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Science / Year: 2022
Title: Evolution of increased complexity and specificity at the dawn of form I Rubiscos.
Authors: Luca Schulz / Zhijun Guo / Jan Zarzycki / Wieland Steinchen / Jan M Schuller / Thomas Heimerl / Simone Prinz / Oliver Mueller-Cajar / Tobias J Erb / Georg K A Hochberg /
Abstract: The evolution of ribulose-1,5-bisphosphate carboxylase/oxygenases (Rubiscos) that discriminate strongly between their substrate carbon dioxide and the undesired side substrate dioxygen was an ...The evolution of ribulose-1,5-bisphosphate carboxylase/oxygenases (Rubiscos) that discriminate strongly between their substrate carbon dioxide and the undesired side substrate dioxygen was an important event for photosynthetic organisms adapting to an oxygenated environment. We use ancestral sequence reconstruction to recapitulate this event. We show that Rubisco increased its specificity and carboxylation efficiency through the gain of an accessory subunit before atmospheric oxygen was present. Using structural and biochemical approaches, we retrace how this subunit was gained and became essential. Our work illuminates the emergence of an adaptation to rising ambient oxygen levels, provides a template for investigating the function of interactions that have remained elusive because of their essentiality, and sheds light on the determinants of specificity in Rubisco.
History
DepositionJan 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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: RubisCO large subunit
B: RubisCO small subunit
C: RubisCO large subunit
D: RubisCO small subunit
E: RubisCO large subunit
F: RubisCO small subunit
G: RubisCO large subunit
H: RubisCO small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,38416
Polymers263,8628
Non-polymers1,5228
Water37,3992076
1
A: RubisCO large subunit
B: RubisCO small subunit
C: RubisCO large subunit
D: RubisCO small subunit
E: RubisCO large subunit
F: RubisCO small subunit
G: RubisCO large subunit
H: RubisCO small subunit
hetero molecules

A: RubisCO large subunit
B: RubisCO small subunit
C: RubisCO large subunit
D: RubisCO small subunit
E: RubisCO large subunit
F: RubisCO small subunit
G: RubisCO large subunit
H: RubisCO small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)530,76732
Polymers527,72416
Non-polymers3,04316
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area88420 Å2
ΔGint-351 kcal/mol
Surface area121520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.873, 131.873, 305.463
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-755-

HOH

21C-806-

HOH

31C-923-

HOH

41C-953-

HOH

51C-999-

HOH

61E-740-

HOH

71E-763-

HOH

81E-890-

HOH

91E-906-

HOH

101E-969-

HOH

-
Components

#1: Protein
RubisCO large subunit


Mass: 53485.637 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Variant (production host): ArcticExpress (DE3) / References: ribulose-bisphosphate carboxylase
#2: Protein
RubisCO small subunit


Mass: 12479.868 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Variant (production host): ArcticExpress (DE3) / References: ribulose-bisphosphate carboxylase
#3: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O13P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2076 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 9.4
Details: Purified enzyme (1.5 mg/mL) in 25 mM Tricine-NaOH, 75 mM NaCl, pH 8.0 was incubated at 3% (v/v) CO2 in air and 30 degrees C for 1 h in the presence of 0.125 mM CABP and 2 mM MgCl2. The ...Details: Purified enzyme (1.5 mg/mL) in 25 mM Tricine-NaOH, 75 mM NaCl, pH 8.0 was incubated at 3% (v/v) CO2 in air and 30 degrees C for 1 h in the presence of 0.125 mM CABP and 2 mM MgCl2. The enzyme was then mixed in a 1:1 ratio with 0.2 M Bis-Tris propane, 20 % (w/v) polyethylene glycol 4000, pH 9.4. Before flash freezing the crystals in liquid nitrogen PEG200 was added to the mother liquor as cryoprotectant to a final concentration of 33 % (w/v).

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.8→19.963 Å / Num. all: 247678 / Num. obs: 247678 / % possible obs: 99.9 % / Redundancy: 13.7 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.128 / Rsym value: 0.123 / Net I/av σ(I): 5.6 / Net I/σ(I): 15.3 / Num. measured all: 3394733
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.913.81.0150.7492040357790.2821.0541.0152.8100
1.9-2.0113.70.6241.2463479339280.1740.6490.6244.5100
2.01-2.1513.80.4021.9439131319180.1120.4170.4026.8100
2.15-2.3213.90.272.7414807297840.0750.2810.279.7100
2.32-2.5513.80.1893.9378509274740.0520.1960.18913100
2.55-2.8513.60.1365.3338362249070.0380.1410.13617.2100
2.85-3.2913.50.097.8299415221130.0250.0940.0924.7100
3.29-4.0213.90.05811.7261860187830.0160.060.05837.7100
4.02-5.6913.40.04813.5198141147360.0130.050.04843.3100
5.69-19.96313.20.0512.210898982560.0140.0520.054397.7

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
XDS20210323data reduction
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6URA

6ura


Resolution: 1.8→19.96 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.52 / Phase error: 14.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1592 1999 81 %
Rwork0.1407 245526 -
obs0.1408 247525 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95 Å2 / Biso mean: 24.804 Å2 / Biso min: 12.67 Å2
Refinement stepCycle: final / Resolution: 1.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18193 0 88 2076 20357
Biso mean--18.55 32.39 -
Num. residues----2273
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.840.23451410.20591734217483
1.84-1.890.20151410.18471732717468
1.89-1.950.18531410.16511734617487
1.95-2.010.19781420.15011736017502
2.01-2.090.15781410.1451739517536
2.09-2.170.16261430.13961744417587
2.17-2.270.17321410.13881741617557
2.27-2.390.1551430.13921742217565
2.39-2.540.16031420.1391750317645
2.54-2.730.16151430.14171753217675
2.73-3.010.15161430.14221758817731
3.01-3.440.17041440.13931763117775
3.44-4.320.1431460.12051782117967
4.32-19.960.13681480.13921839918547
Refinement TLS params.Method: refined / Origin x: 78.4317 Å / Origin y: 77.4245 Å / Origin z: 74.0743 Å
111213212223313233
T0.1431 Å2-0.0214 Å2-0.0055 Å2-0.1609 Å20.0033 Å2--0.1642 Å2
L0.1248 °2-0.0033 °2-0.004 °2-0.119 °2-0.0083 °2--0.2384 °2
S0.0007 Å °0.017 Å °0.0113 Å °0.008 Å °-0.0051 Å °-0.0483 Å °-0.0344 Å °0.0676 Å °0.0044 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 475
2X-RAY DIFFRACTION1allA500 - 520
3X-RAY DIFFRACTION1allB1 - 102
4X-RAY DIFFRACTION1allC9 - 475
5X-RAY DIFFRACTION1allC500 - 520
6X-RAY DIFFRACTION1allD1 - 102
7X-RAY DIFFRACTION1allE10 - 475
8X-RAY DIFFRACTION1allE500 - 520
9X-RAY DIFFRACTION1allF1 - 102
10X-RAY DIFFRACTION1allG10 - 475
11X-RAY DIFFRACTION1allG500 - 520
12X-RAY DIFFRACTION1allH1 - 102
13X-RAY DIFFRACTION1allS1 - 2076

+
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://pdbjlvh1.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