[English] 日本語
Yorodumi
- PDB-8i8p: Crystal structure of the complex of phosphopantetheine adenylyltr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8i8p
TitleCrystal structure of the complex of phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Dephosphocoenzyme-A at 2.19 A resolution.
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / coaD / PPAT / COENZYME A biosynthesis
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 / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
DEPHOSPHO COENZYME A / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsAhmad, N. / Viswanathan, V. / Gupta, A. / Sharma, P. / Sharma, S. / Singh, T.P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the complex of phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Dephosphocoenzyme-A at 2.19 A resolution.
Authors: Ahmad, N. / Viswanathan, V. / Gupta, A. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionFeb 4, 2023Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 12, 2023ID: 6KYG
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4186
Polymers18,4791
Non-polymers9395
Water1,60389
1
A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,83712
Polymers36,9582
Non-polymers1,87910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation85_544y+1/4,x-1/4,-z-1/41
Buried area6070 Å2
ΔGint-122 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.038, 217.038, 217.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 18479.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Gene: coaD, HMPREF0010_01342
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D0C9M9, pantetheine-phosphate adenylyltransferase

-
Non-polymers , 5 types, 94 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-COD / DEPHOSPHO COENZYME A


Mass: 687.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H35N7O13P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.76 Å3/Da / Density % sol: 78.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1M LITHIUM SULPHATE, 2M AMMONIUM SULPHATE, 0.1M SODIUM CITRATE, PH 5.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97199 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97199 Å / Relative weight: 1
ReflectionResolution: 2.19→125.307 Å / Num. obs: 22090 / % possible obs: 95.48 % / Redundancy: 20 % / CC1/2: 0.99 / Net I/σ(I): 16.2
Reflection shellResolution: 2.19→2.25 Å / Num. unique obs: 1044 / CC1/2: 0.631

-
Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→125.307 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: FREE R-VALUE / ESU R: 0.14 / ESU R Free: 0.14
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2367 1044 4.726 %
Rwork0.2011 21046 -
all0.203 --
obs-22090 95.582 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 63.419 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.19→125.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 56 89 1450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121391
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161296
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.651886
X-RAY DIFFRACTIONr_angle_other_deg1.1051.5712970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3815162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.226512
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.3451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1710224
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.6351067
X-RAY DIFFRACTIONr_chiral_restr0.0950.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021605
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02340
X-RAY DIFFRACTIONr_nbd_refined0.2220.2316
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2240.21190
X-RAY DIFFRACTIONr_nbtor_refined0.1950.2699
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.2788
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2920.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0770.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1960.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2950.218
X-RAY DIFFRACTIONr_nbd_other0.2960.2113
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.216
X-RAY DIFFRACTIONr_mcbond_it6.4556.008651
X-RAY DIFFRACTIONr_mcbond_other6.4496.011651
X-RAY DIFFRACTIONr_mcangle_it8.76410.786812
X-RAY DIFFRACTIONr_mcangle_other8.80210.789813
X-RAY DIFFRACTIONr_scbond_it9.3997.33740
X-RAY DIFFRACTIONr_scbond_other9.3377.306733
X-RAY DIFFRACTIONr_scangle_it13.61212.9621074
X-RAY DIFFRACTIONr_scangle_other13.61112.9251063
X-RAY DIFFRACTIONr_lrange_it15.80665.6491622
X-RAY DIFFRACTIONr_lrange_other15.65264.5771593
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.19-2.2470.369640.34510060.34716720.9250.91263.99520.332
2.247-2.3090.423570.32812100.33216390.8990.92677.30320.306
2.309-2.3760.421740.31614600.32115790.9090.93897.15010.282
2.376-2.4490.312660.30714740.30715400.9430.9471000.269
2.449-2.5290.306720.28514180.28614900.9450.9581000.239
2.529-2.6180.309510.26313950.26414460.9550.9611000.214
2.618-2.7170.288610.25313350.25513960.9590.9681000.211
2.717-2.8270.229800.20912730.2113530.9660.9731000.178
2.827-2.9530.291530.21912530.22213060.9520.9691000.195
2.953-3.0970.345520.23411930.23812450.9180.9651000.214
3.097-3.2640.296560.2311320.23311880.9430.9691000.217
3.264-3.4620.287480.21610800.21811280.9550.9761000.211
3.462-3.7010.284550.21610130.21910680.9590.9781000.219
3.701-3.9970.233580.1959440.19710020.970.981000.206
3.997-4.3790.168450.1638830.1639280.9840.9861000.189
4.379-4.8950.14430.1258070.1268500.9840.991000.151
4.895-5.650.191330.1777290.1787620.9870.9821000.217
5.65-6.9170.304320.2066180.2116500.9520.9761000.249
6.917-9.7670.173340.1454960.1475310.9840.98899.81170.201
9.767-125.3070.245100.2413270.2413380.9760.95199.70410.403

+
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