[English] 日本語
Yorodumi
- PDB-3l92: Phosphopantetheine adenylyltransferase from Yersinia pestis compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3l92
TitlePhosphopantetheine adenylyltransferase from Yersinia pestis complexed with coenzyme A.
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / structural genomics / phosphopantetheine adenylyltransferase / coenzyme A / ATP-binding / Coenzyme A biosynthesis / Nucleotide-binding / Nucleotidyltransferase / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP 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
COENZYME A / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsOsipiuk, J. / Maltseva, N. / Makowska-grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: X-ray crystal structure of phosphopantetheine adenylyltransferase from Yersinia pestis.
Authors: Osipiuk, J. / Maltseva, N. / Makowska-grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionJan 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 1, 2014Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7162
Polymers17,9481
Non-polymers7681
Water2,990166
1
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)112,29312
Polymers107,6886
Non-polymers4,6056
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area22730 Å2
ΔGint-131 kcal/mol
Surface area36490 Å2
MethodPISA
2
A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1476
Polymers53,8443
Non-polymers2,3033
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7840 Å2
ΔGint-33 kcal/mol
Surface area21770 Å2
MethodPISA
3
A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4314
Polymers35,8962
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area4380 Å2
ΔGint-21 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.820, 114.820, 119.074
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-255-

HOH

-
Components

#1: Protein Phosphopantetheine adenylyltransferase / Pantetheine-phosphate adenylyltransferase / PPAT / Dephospho-CoA pyrophosphorylase


Mass: 17948.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: coaD, kdtB, y0088, YPO0053, YP_0054 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8ZJN9, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 4.21 Å3/Da / Density % sol: 70.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1 M tri-sodium citrate, 0.1 M sodium cacodylate, 0.01 M coenzyme A, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.89→38.2 Å / Num. all: 24323 / Num. obs: 24323 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.33 / Net I/σ(I): 9.5
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.836 / Mean I/σ(I) obs: 3.81 / Num. unique all: 1205 / Χ2: 1.293 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H1T

1h1t


Resolution: 1.89→38.2 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.142 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.097 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1239 5.1 %RANDOM
Rwork0.164 ---
all0.165 24310 --
obs0.165 24310 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 68.38 Å2 / Biso mean: 26.902 Å2 / Biso min: 12.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å2-0.4 Å20 Å2
2---0.79 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 1.89→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 48 166 1457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221480
X-RAY DIFFRACTIONr_angle_refined_deg1.8662.0612044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0555194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32323.650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60315271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.172157
X-RAY DIFFRACTIONr_chiral_restr0.1230.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211046
X-RAY DIFFRACTIONr_mcbond_it1.0551.5855
X-RAY DIFFRACTIONr_mcangle_it1.8721409
X-RAY DIFFRACTIONr_scbond_it2.9523625
X-RAY DIFFRACTIONr_scangle_it4.4784.5616
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 89 -
Rwork0.237 1687 -
all-1776 -
obs-1776 99.83 %
Refinement TLS params.Method: refined / Origin x: 4.7857 Å / Origin y: 18.5394 Å / Origin z: 45.5202 Å
111213212223313233
T0.0889 Å2-0.0216 Å2-0.009 Å2-0.013 Å20.0239 Å2--0.0643 Å2
L1.1444 °2-0.3845 °2-0.2485 °2-1.7906 °2-0.6139 °2--1.3905 °2
S-0.0247 Å °0.0055 Å °0.0225 Å °-0.2033 Å °0.0112 Å °-0.1161 Å °-0.0309 Å °-0.0047 Å °0.0135 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 159
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A160 - 326

+
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