[English] 日本語
Yorodumi
- PDB-1qjc: Phosphopantetheine Adenylyltransferase from Escherichia coli in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qjc
TitlePhosphopantetheine Adenylyltransferase from Escherichia coli in complex with 4'-phosphopantetheine
ComponentsPHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
KeywordsCOENZYME A BIOSYNTHESIS / TRANSFERASE / NUCLEOTIDYLTRANSFERASE
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Phosphopantetheine adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4'-PHOSPHOPANTETHEINE / Phosphopantetheine adenylyltransferase / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsIzard, T.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The Crystal Structures of Phosphopantetheine Adenylyltransferase with Bound Substrates Reveal the Enzyme'S Catalytic Mechanism
Authors: Izard, T.
History
DepositionJun 23, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
B: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2968
Polymers35,4572
Non-polymers8396
Water4,990277
1
A: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
B: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
hetero molecules

A: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
B: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
hetero molecules

A: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
B: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,88724
Polymers106,3716
Non-polymers2,51618
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area18260 Å2
ΔGint-142.8 kcal/mol
Surface area42370 Å2
MethodPQS
Unit cell
Length a, b, c (Å)135.331, 135.331, 135.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.066398, 0.128795, -0.989446), (0.084424, -0.987353, -0.134188), (-0.994215, -0.092443, 0.054685)
Vector: 63.9004, 67.7114, 67.0611)
DetailsBIOLOGICAL_UNIT: HOMOHEXAMER

-
Components

#1: Protein PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE / PPAT / PANTETHEINE-PHOSPHATE ADENYLYLTRANSFERASE / DEPHOSPHO-COA PYROPHOSPHORYLASE


Mass: 17728.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli)
References: UniProt: P23875, UniProt: P0A6I6*PLUS, pantetheine-phosphate adenylyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: REVERSIBLY TRANSFERS AN ADENYLYL GROUP FROM ATP TO 4'- PHOSPHOPANTETHEINE, YIELDING ...FUNCTION: REVERSIBLY TRANSFERS AN ADENYLYL GROUP FROM ATP TO 4'- PHOSPHOPANTETHEINE, YIELDING DEPHOSPHO-COA (DPCOA) AND PYROPHOSPHATE. CATALYTIC ACTIVITY: ATP + PANTETHEINE 4'-PHOSPHATE = DIPHOSPHATE + DEPHOSPHO-COA. PATHWAY: COENZYME A (COA) BIOSYNTHESIS; FOURTH STEP. SUBUNIT: HOMOHEXAMER. SUBCELLULAR LOCATION: CYTOPLASMIC. SIMILARITY: BELONGS TO THE COAD FAMILY.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57 %
Crystal growpH: 5 / Details: pH 5.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
DetectorDetector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 33838 / % possible obs: 86.3 % / Observed criterion σ(I): 1 / Redundancy: 20.02 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 44.2
Reflection shellResolution: 1.8→1.91 Å / Rmerge(I) obs: 0.409 / % possible all: 51.5

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B6T

1b6t


Resolution: 1.63→67.67 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3212744.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2569 5.1 %RANDOM
Rwork0.216 ---
obs0.216 50637 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.226 Å2 / ksol: 0.363602 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.63→67.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 47 277 2796
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.881.5
X-RAY DIFFRACTIONc_mcangle_it1.492
X-RAY DIFFRACTIONc_scbond_it1.392
X-RAY DIFFRACTIONc_scangle_it2.12.5
LS refinement shellResolution: 1.63→1.73 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 420 5.4 %
Rwork0.301 7387 -
obs--92.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER-TOPOLOGY
X-RAY DIFFRACTION3PNS.PARPNS.TOP

+
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