[English] 日本語
Yorodumi
- PDB-1u7z: Phosphopantothenoylcysteine synthetase from E. coli, 4'-phosphopa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u7z
TitlePhosphopantothenoylcysteine synthetase from E. coli, 4'-phosphopantothenoyl-CMP complex
ComponentsCoenzyme A biosynthesis bifunctional protein coaBC
KeywordsLIGASE / Coenzyme A biosynthesis
Function / homology
Function and homology information


phosphopantothenoylcysteine decarboxylase complex / pantothenate catabolic process / phosphopantothenoylcysteine decarboxylase / phosphopantothenate-cysteine ligase (CTP) / phosphopantothenate--cysteine ligase activity / phosphopantothenoylcysteine decarboxylase activity / coenzyme A biosynthetic process / FMN binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
CoaB-like / Coenzyme A biosynthesis bifunctional protein CoaBC / DNA/pantothenate metabolism flavoprotein, C-terminal / CoaB-like superfamily / DNA / pantothenate metabolism flavoprotein / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PMT / Coenzyme A biosynthesis bifunctional protein CoaBC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsStanitzek, S. / Augustin, M.A. / Huber, R. / Kupke, T. / Steinbacher, S.
CitationJournal: STRUCTURE / Year: 2004
Title: Structural Basis of CTP-Dependent Peptide Bond Formation in Coenzyme A Biosynthesis Catalyzed by Escherichia coli PPC Synthetase
Authors: Stanitzek, S. / Augustin, M.A. / Huber, R. / Kupke, T. / Steinbacher, S.
History
DepositionAug 4, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: 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: Coenzyme A biosynthesis bifunctional protein coaBC
B: Coenzyme A biosynthesis bifunctional protein coaBC
C: Coenzyme A biosynthesis bifunctional protein coaBC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3136
Polymers74,5003
Non-polymers1,8133
Water4,648258
1
A: Coenzyme A biosynthesis bifunctional protein coaBC
B: Coenzyme A biosynthesis bifunctional protein coaBC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8754
Polymers49,6672
Non-polymers1,2092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-13 kcal/mol
Surface area19350 Å2
MethodPISA
2
C: Coenzyme A biosynthesis bifunctional protein coaBC
hetero molecules

C: Coenzyme A biosynthesis bifunctional protein coaBC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8754
Polymers49,6672
Non-polymers1,2092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)43.627, 142.584, 244.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Coenzyme A biosynthesis bifunctional protein coaBC


Mass: 24833.348 Da / Num. of mol.: 3
Fragment: Phosphopantothenoylcysteine synthetase(residues 181-406)
Mutation: N210D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABQ0, phosphopantothenate-cysteine ligase (CTP)
#2: Chemical ChemComp-PMT / PHOSPHORIC ACID MONO-[3-(3-{[5-(4-AMINO-2-OXO-2H-PYRIMIDIN-1-YL)-3,4- DIHYDROXY-TETRAHYDRO-FURAN-2- YLMETHOXY]-HYDROXY-PHOSPHORYLOXY}-3-OXO-PROPYLCARBAMOYL)-3-HYDROXY-2,2- DIMETHYL-PROPYL] ESTER / 4'-PHOSPHOPANTOTHENOYL- CYTIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 604.396 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H30N4O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: PEG 3000, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9789 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 32347 / Num. obs: 32347 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.088
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.297 / % possible all: 97.1

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U7U

1u7u


Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1603 -random
Rwork0.196 ---
all0.203 32347 --
obs0.203 32347 93.4 %-
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5038 0 117 258 5413
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.67

+
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