[English] 日本語
Yorodumi
- PDB-6v3o: Crystal structure of the T-state of maize C4-phosphoenolpyruvate ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v3o
TitleCrystal structure of the T-state of maize C4-phosphoenolpyruvate carboxylase in complex with citrate
ComponentsPhosphoenolpyruvate carboxylase
KeywordsLYASE / C4 metabolism / allosteric regulation / R and T states / Plant Protein
Function / homology
Function and homology information


response to cytokinin / phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / response to nitrate / leaf development / response to ammonium ion / carbon fixation / tricarboxylic acid cycle / photosynthesis / cytoplasm / cytosol
Similarity search - Function
Phosphoenolpyruvate carboxylase, Lys active site / Phosphoenolpyruvate carboxylase / Phosphoenolpyruvate carboxylase, bacterial/plant-type / Phosphoenolpyruvate carboxylase, His active site / Phosphoenolpyruvate carboxylase / Phosphoenolpyruvate carboxylase active site 2. / Phosphoenolpyruvate carboxylase active site 1. / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
CITRATE ANION / Phosphoenolpyruvate carboxylase 1 / phosphoenolpyruvate carboxylase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.909 Å
AuthorsCarrizosa-Carbajal, E.I. / Munoz-Clares, R.A. / Gonzalez-Segura, L.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IN227920 Mexico
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Two new T-state crystal structures of maize C 4 -phosphoenolpyruvate carboxylase reveal and suggest novel structural features of the allosteric regulation and carboxylation step.
Authors: Carrizosa-Carbajal, E.I. / Gonzalez-Segura, L. / Munoz-Clares, R.A.
History
DepositionNov 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 17, 2023Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.grant_number
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Sep 11, 2024Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoenolpyruvate carboxylase
B: Phosphoenolpyruvate carboxylase
C: Phosphoenolpyruvate carboxylase
D: Phosphoenolpyruvate carboxylase
E: Phosphoenolpyruvate carboxylase
F: Phosphoenolpyruvate carboxylase
G: Phosphoenolpyruvate carboxylase
H: Phosphoenolpyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)879,42439
Polymers875,8728
Non-polymers3,55231
Water1086
1
A: Phosphoenolpyruvate carboxylase
B: Phosphoenolpyruvate carboxylase
C: Phosphoenolpyruvate carboxylase
D: Phosphoenolpyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,77319
Polymers437,9364
Non-polymers1,83715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15860 Å2
ΔGint-170 kcal/mol
Surface area136390 Å2
MethodPISA
2
E: Phosphoenolpyruvate carboxylase
F: Phosphoenolpyruvate carboxylase
G: Phosphoenolpyruvate carboxylase
H: Phosphoenolpyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,65120
Polymers437,9364
Non-polymers1,71516
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16440 Å2
ΔGint-230 kcal/mol
Surface area135430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.692, 217.976, 173.569
Angle α, β, γ (deg.)90.000, 91.050, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Phosphoenolpyruvate carboxylase


Mass: 109484.016 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ppc1 / Plasmid: pET32-ZmPEPC-C4 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): RIL
References: UniProt: Q84KR7, UniProt: P04711*PLUS, phosphoenolpyruvate carboxylase

-
Non-polymers , 5 types, 37 molecules

#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M TRI-SODIUM CITRATE/KOH, 0.2M AMMONIUM SULFATE, 12% PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.909→49.2 Å / Num. obs: 225088 / % possible obs: 98.46 % / Redundancy: 3.3 % / CC1/2: 0.65 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.08 / Net I/σ(I): 5.9
Reflection shellResolution: 2.91→3.07 Å / Rmerge(I) obs: 0.523 / Num. unique obs: 103014

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALA3.3.20data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U2T

6u2t


Resolution: 2.909→49.198 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2495 11280 5.01 %
Rwork0.2184 213771 -
obs0.2199 225051 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.39 Å2 / Biso mean: 60.6344 Å2 / Biso min: 34.53 Å2
Refinement stepCycle: final / Resolution: 2.909→49.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms59474 0 208 6 59688
Biso mean--69.8 44.57 -
Num. residues----7480
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.909-2.94210.37153060.3193573779
2.9421-2.97670.3363910.27557121100
2.9767-3.0130.32613780.27227228100
3.013-3.05110.30893460.2696722599
3.0511-3.09130.29753530.2588717099
3.0913-3.13360.31283810.2637721499
3.1336-3.17840.29514080.2648711099
3.1784-3.22580.33333900.2703709899
3.2258-3.27620.29223560.2642720998
3.2762-3.32990.32073920.2636703898
3.3299-3.38730.2893380.2582707198
3.3873-3.44890.29483830.2583706597
3.4489-3.51520.29773810.2521707898
3.5152-3.58690.27073580.23547174100
3.5869-3.66490.25334170.2327161100
3.6649-3.75010.2553950.23257247100
3.7501-3.84390.28273610.23367222100
3.8439-3.94780.2513660.2317263100
3.9478-4.06390.25113590.21827194100
4.0639-4.1950.24753900.21637200100
4.195-4.34480.24174140.209717899
4.3448-4.51870.25913620.21017215100
4.5187-4.72420.24513880.2064716699
4.7242-4.9730.24413400.2023713698
4.973-5.28430.22053870.2063704697
5.2843-5.69170.24623930.21057248100
5.6917-6.26350.23823840.22087252100
6.2635-7.16740.2213950.19537253100
7.1674-9.02110.16073570.1529725699
9.0211-49.1980.16474110.1511719698

+
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