[English] 日本語
Yorodumi
- PDB-1xeb: Crystal Structure of an Acyl-CoA N-acyltransferase from Pseudomon... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xeb
TitleCrystal Structure of an Acyl-CoA N-acyltransferase from Pseudomonas aeruginosa
Componentshypothetical protein PA0115
KeywordsTRANSFERASE / Midwest Center for Structural Genomics / MCSG / Structural Genomics / Protein Structure Initiative / PSI / APC22065
Function / homology
Function and homology information


N-acetyltransferase activity
Similarity search - Function
Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsBertero, M.G. / Walker, J.R. / Skarina, T. / Gorodichtchenskaia, E. / Joachimiak, A. / Edwards, A.E. / Savchenko, A. / Strynadka, N. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of an Acyl-CoA N-acyltransferase from Pseudomonas aeruginosa
Authors: Bertero, M.G. / Walker, J.R. / Skarina, T. / Gorodichtchenskaia, E. / Joachimiak, A. / Edwards, A.E. / Savchenko, A. / Strynadka, N.
History
DepositionSep 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein PA0115
B: hypothetical protein PA0115
C: hypothetical protein PA0115
D: hypothetical protein PA0115
E: hypothetical protein PA0115
F: hypothetical protein PA0115
G: hypothetical protein PA0115
H: hypothetical protein PA0115


Theoretical massNumber of molelcules
Total (without water)137,9788
Polymers137,9788
Non-polymers00
Water3,999222
1
A: hypothetical protein PA0115


Theoretical massNumber of molelcules
Total (without water)17,2471
Polymers17,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: hypothetical protein PA0115


Theoretical massNumber of molelcules
Total (without water)17,2471
Polymers17,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: hypothetical protein PA0115


Theoretical massNumber of molelcules
Total (without water)17,2471
Polymers17,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: hypothetical protein PA0115


Theoretical massNumber of molelcules
Total (without water)17,2471
Polymers17,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: hypothetical protein PA0115


Theoretical massNumber of molelcules
Total (without water)17,2471
Polymers17,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: hypothetical protein PA0115


Theoretical massNumber of molelcules
Total (without water)17,2471
Polymers17,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
G: hypothetical protein PA0115


Theoretical massNumber of molelcules
Total (without water)17,2471
Polymers17,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
H: hypothetical protein PA0115


Theoretical massNumber of molelcules
Total (without water)17,2471
Polymers17,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
9
A: hypothetical protein PA0115
D: hypothetical protein PA0115


Theoretical massNumber of molelcules
Total (without water)34,4942
Polymers34,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-20 kcal/mol
Surface area14460 Å2
MethodPISA
10
E: hypothetical protein PA0115
F: hypothetical protein PA0115


Theoretical massNumber of molelcules
Total (without water)34,4942
Polymers34,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-19 kcal/mol
Surface area14360 Å2
MethodPISA
11
B: hypothetical protein PA0115
C: hypothetical protein PA0115


Theoretical massNumber of molelcules
Total (without water)34,4942
Polymers34,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-20 kcal/mol
Surface area14620 Å2
MethodPISA
12
G: hypothetical protein PA0115
H: hypothetical protein PA0115


Theoretical massNumber of molelcules
Total (without water)34,4942
Polymers34,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-19 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.397, 138.397, 136.486
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein
hypothetical protein PA0115 / Acyl-CoA N-acyltransferase / APC22065


Mass: 17247.238 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA01 / Plasmid: modified PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I717
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.761 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: NH4Cl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979398 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jun 20, 2004
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979398 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 121434 / Num. obs: 121434 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 16.5
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.7 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→29.89 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3463680.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 4765 8.2 %RANDOM
Rwork0.232 ---
obs0.232 58089 91.9 %-
all-58089 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.2774 Å2 / ksol: 0.322948 e/Å3
Displacement parametersBiso mean: 37.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å23.16 Å20 Å2
2---0.7 Å20 Å2
3---1.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.35→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9480 0 0 222 9702
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 667 8.1 %
Rwork0.261 7528 -
obs--78.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.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