[English] 日本語
Yorodumi
- PDB-6yvb: Arabidopsis aspartate transcarbamoylase complex with carbamoyl ph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yvb
TitleArabidopsis aspartate transcarbamoylase complex with carbamoyl phosphate
ComponentsPYRB
KeywordsPLANT PROTEIN / Transferase / chloroplast / pyrimidine de novo biosynthesis
Function / homology
Function and homology information


aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / cellular response to phosphate starvation / amino acid metabolic process / chloroplast stroma / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / chloroplast
Similarity search - Function
Aspartate carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold ...Aspartate carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / aspartate carbamoyltransferase / Aspartate carbamoyltransferase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.826 Å
AuthorsRamon Maiques, S. / Del Cano Ochoa, F. / Bellin, L. / Mohlmann, T.
Funding support Spain, Germany, 4items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2016-80570-R Spain
Spanish Ministry of Science, Innovation, and UniversitiesRTI2018-098084-B-100 Spain
German Research Foundation (DFG)Mo 1032/4-1) Germany
German Research Foundation (DFG)IRTG 1830 Germany
CitationJournal: Nat Commun / Year: 2021
Title: Mechanisms of feedback inhibition and sequential firing of active sites in plant aspartate transcarbamoylase.
Authors: Bellin, L. / Del Cano-Ochoa, F. / Velazquez-Campoy, A. / Mohlmann, T. / Ramon-Maiques, S.
History
DepositionApr 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PYRB
B: PYRB
C: PYRB
D: PYRB
E: PYRB
F: PYRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,22540
Polymers223,1316
Non-polymers3,09434
Water24,0321334
1
A: PYRB
B: PYRB
C: PYRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,41524
Polymers111,5653
Non-polymers1,84921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-47 kcal/mol
Surface area35630 Å2
MethodPISA
2
D: PYRB
E: PYRB
F: PYRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,81016
Polymers111,5653
Non-polymers1,24513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9930 Å2
ΔGint-42 kcal/mol
Surface area35440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.268, 109.481, 212.042
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
PYRB


Mass: 37188.488 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AXX17_At3g21670 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A178VJE3, UniProt: P49077*PLUS
#2: Chemical
ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: CH4NO5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1334 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: Protein at 5 mg/ml in buffer 20 mM Tris pH 7.0, 0.1 M NaCl, 2% glycerol, 0.2 mM tris(2-carboxyethyl) phosphine (TCEP), with 10 mM carbamoyl phosphate. Crystallization solution: 25% PEG3350, ...Details: Protein at 5 mg/ml in buffer 20 mM Tris pH 7.0, 0.1 M NaCl, 2% glycerol, 0.2 mM tris(2-carboxyethyl) phosphine (TCEP), with 10 mM carbamoyl phosphate. Crystallization solution: 25% PEG3350, 0.2 M Li2SO4 and 0.1 M bis-tris pH 5.5. Cryo-conditions achieved by increasing glycerol concentration up to 20% in presence of carbamoyl phosphate.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.826→76.278 Å / Num. obs: 212623 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 17.6
Reflection shellResolution: 1.826→1.93 Å / Rmerge(I) obs: 1.058 / Num. unique obs: 30789 / CC1/2: 0.704

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YS6

6ys6


Resolution: 1.826→76.278 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.192 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.113 / ESU R Free: 0.114
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.213 10800 5.082 %
Rwork0.172 --
all0.174 --
obs-212513 99.906 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.606 Å2
Baniso -1Baniso -2Baniso -3
1-1.068 Å20 Å20 Å2
2---0.039 Å20 Å2
3----1.028 Å2
Refinement stepCycle: LAST / Resolution: 1.826→76.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14733 0 196 1334 16263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01315633
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714920
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.64521109
X-RAY DIFFRACTIONr_angle_other_deg1.4071.58134518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89651996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.03121.683814
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.809152863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.37715126
X-RAY DIFFRACTIONr_chiral_restr0.0830.22040
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217680
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023330
X-RAY DIFFRACTIONr_nbd_refined0.1990.23081
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.214261
X-RAY DIFFRACTIONr_nbtor_refined0.1620.27477
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.27254
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.21163
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.080.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2250.218
X-RAY DIFFRACTIONr_nbd_other0.1880.2102
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.231
X-RAY DIFFRACTIONr_mcbond_it3.3033.7737820
X-RAY DIFFRACTIONr_mcbond_other3.3033.7737818
X-RAY DIFFRACTIONr_mcangle_it4.2125.6359837
X-RAY DIFFRACTIONr_mcangle_other4.2125.6359838
X-RAY DIFFRACTIONr_scbond_it4.2534.1737813
X-RAY DIFFRACTIONr_scbond_other4.2534.1747814
X-RAY DIFFRACTIONr_scangle_it6.1056.08311263
X-RAY DIFFRACTIONr_scangle_other6.1056.08311264
X-RAY DIFFRACTIONr_lrange_it7.50945.00917585
X-RAY DIFFRACTIONr_lrange_other7.48244.63417321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.826-1.8740.2977790.29714777X-RAY DIFFRACTION99.8652
1.874-1.9250.3077550.2714447X-RAY DIFFRACTION99.9868
1.925-1.9810.2937470.25114055X-RAY DIFFRACTION99.973
1.981-2.0420.2836530.2313653X-RAY DIFFRACTION99.986
2.042-2.1090.2627350.2113213X-RAY DIFFRACTION99.9857
2.109-2.1830.2366810.19512832X-RAY DIFFRACTION99.9926
2.183-2.2650.2396840.18212314X-RAY DIFFRACTION99.9769
2.265-2.3580.236820.17911864X-RAY DIFFRACTION99.9681
2.358-2.4620.2276340.17311399X-RAY DIFFRACTION99.9751
2.462-2.5820.2296150.17310899X-RAY DIFFRACTION99.9826
2.582-2.7220.2155630.16610447X-RAY DIFFRACTION99.9728
2.722-2.8870.2245410.1659861X-RAY DIFFRACTION99.9712
2.887-3.0860.2115030.179245X-RAY DIFFRACTION99.9487
3.086-3.3330.2014760.178682X-RAY DIFFRACTION99.9018
3.333-3.6510.214070.1728014X-RAY DIFFRACTION99.9644
3.651-4.0810.183640.1487282X-RAY DIFFRACTION99.9477
4.081-4.7120.1643970.136403X-RAY DIFFRACTION99.7945
4.712-5.7680.1822800.155497X-RAY DIFFRACTION99.7238
5.768-8.1450.2282170.1824292X-RAY DIFFRACTION99.6684
8.145-76.2780.217870.1662538X-RAY DIFFRACTION99.2814

+
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