[English] 日本語
Yorodumi
- PDB-8qmw: Non-obligately L8S8-complex forming RubisCO derived from ancestra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qmw
TitleNon-obligately L8S8-complex forming RubisCO derived from ancestral sequence reconstruction and rational engineering in L8S8 complex with substitutions R269W, E271R, L273N
Components
  • RubisCO large subunit
  • RubisCO small subunit
KeywordsLYASE / RubisCO / CABP / ancestral
Function / homology2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsZarzycki, J. / Schulz, L. / Erb, T.J. / Hochberg, G.K.A.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
Joachim Herz Stiftung Germany
Citation
Journal: Embo J. / Year: 2025
Title: Layered entrenchment maintains essentiality in the evolution of Form I Rubisco complexes.
Authors: Schulz, L. / Zarzycki, J. / Steinchen, W. / Hochberg, G.K.A. / Erb, T.J.
#1: Journal: Biorxiv / Year: 2024
Title: Layered entrenchment maintains essentiality in protein-protein interactions
Authors: Schulz, L. / Zarzycki, J. / Steinchen, W. / Hochberg, G.K.A. / Erb, T.J.
History
DepositionSep 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification
Revision 1.2Jan 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)256,34717
Polymers254,5438
Non-polymers1,8049
Water36,3002015
1
A: RubisCO large subunit
B: RubisCO large subunit
C: RubisCO large subunit
D: RubisCO large subunit
E: RubisCO small subunit
F: RubisCO small subunit
G: RubisCO small subunit
H: RubisCO small subunit
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)512,69434
Polymers509,08616
Non-polymers3,60818
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area86850 Å2
ΔGint-341 kcal/mol
Surface area117290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.010, 106.440, 108.490
Angle α, β, γ (deg.)90.00, 113.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-701-

HOH

21B-979-

HOH

-
Components

-
Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
RubisCO large subunit


Mass: 51155.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / 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(DE3) (bacteria)

-
Sugars , 1 types, 4 molecules

#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

-
Non-polymers , 3 types, 2020 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C11H26N2O6 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2015 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.1
Details: Purified enzyme (9 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 hour in the presence of 0.35 mM CABP and 5.6 mM MgCl2. The ...Details: Purified enzyme (9 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 hour in the presence of 0.35 mM CABP and 5.6 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 9.1. Drops were supplemented with 25 % (v/v) PEG200 before flash freezing crystals in lquid nitrogen.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.6888 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Dec 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.75→24.88 Å / Num. obs: 213396 / % possible obs: 98.5 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.133 / Net I/σ(I): 11.11
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.75-1.80.673156470.820.7241
1.8-1.840.565153510.870.6081
1.84-1.90.47149080.9050.5051
1.9-1.960.395144390.930.4261
1.96-2.020.333140150.9490.3591
2.02-2.090.278135740.9670.31
2.09-2.170.247131370.9710.2661
2.17-2.260.21126210.9780.2271
2.26-2.360.179121540.9850.1921
2.36-2.470.16116010.9880.1731
2.47-2.610.141110670.990.1521
2.61-2.770.122104800.9920.1311
2.77-2.960.10998430.9940.1171
2.96-3.20.09291120.9950.0991
3.2-3.50.07284570.9960.0781
3.5-3.910.05976810.9980.0631
3.91-4.520.05267670.9980.0561
4.52-5.530.05257270.9980.0561
5.53-7.830.05844230.9970.0631
7.83-24.880.05123920.9980.0551

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→24.88 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1745 1999 0.94 %
Rwork0.1448 --
obs0.1451 213375 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17595 0 107 2015 19717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01318162
X-RAY DIFFRACTIONf_angle_d1.14824650
X-RAY DIFFRACTIONf_dihedral_angle_d12.9176635
X-RAY DIFFRACTIONf_chiral_restr0.0732564
X-RAY DIFFRACTIONf_plane_restr0.0133234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.21111410.188914957X-RAY DIFFRACTION98
1.79-1.840.2121420.178915023X-RAY DIFFRACTION98
1.84-1.90.19351430.170715013X-RAY DIFFRACTION98
1.9-1.960.19141420.156415018X-RAY DIFFRACTION98
1.96-2.030.2171420.154815041X-RAY DIFFRACTION99
2.03-2.110.20011420.15315040X-RAY DIFFRACTION98
2.11-2.20.21181430.14815029X-RAY DIFFRACTION98
2.2-2.320.18561420.145515081X-RAY DIFFRACTION99
2.32-2.470.1811440.144515193X-RAY DIFFRACTION99
2.47-2.660.19141430.146415096X-RAY DIFFRACTION99
2.66-2.920.17781430.142815169X-RAY DIFFRACTION99
2.92-3.350.16171430.1415110X-RAY DIFFRACTION99
3.35-4.210.13871450.122715275X-RAY DIFFRACTION99
4.21-24.880.14721440.141515331X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 22.7726 Å / Origin y: 69.78 Å / Origin z: 3.7322 Å
111213212223313233
T0.1347 Å2-0.0008 Å2-0.0015 Å2-0.1591 Å20.0004 Å2--0.149 Å2
L0.0369 °2-0.0065 °2-0.0022 °2-0.1335 °2-0.0013 °2--0.0321 °2
S-0.0007 Å °0.0013 Å °0.0016 Å °0.005 Å °-0.0006 Å °-0.0217 Å °0.0001 Å °-0.0022 Å °0.0016 Å °
Refinement TLS groupSelection details: all

+
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