[English] 日本語
Yorodumi
- PDB-1y9k: IAA acetyltransferase from Bacillus cereus ATCC 14579 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1y9k
TitleIAA acetyltransferase from Bacillus cereus ATCC 14579
ComponentsIAA acetyltransferase
KeywordsTRANSFERASE / structural genomics / Midwest Center for Structural Genomics (MCSG) / Bacillus cereus ATCC 14579 / IAA acetyltransferase / acetyltransferase / PSI / Protein Structure Initiative
Function / homology
Function and homology information


N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
: / Acetyltransferase (GNAT) family / 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
IAA acetyltransferase
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.39 Å
AuthorsNocek, B.P. / Osipiuk, J. / Li, H. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: A crystal structure of IAA acetyltransferase from Bacillus cereus
Authors: Nocek, B.P. / Osipiuk, J. / Li, H. / Collart, F. / Joachimiak, A.
History
DepositionDec 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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: IAA acetyltransferase
B: IAA acetyltransferase
C: IAA acetyltransferase
D: IAA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)71,1914
Polymers71,1914
Non-polymers00
Water5,044280
1
A: IAA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)17,7981
Polymers17,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: IAA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)17,7981
Polymers17,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: IAA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)17,7981
Polymers17,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: IAA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)17,7981
Polymers17,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.122, 70.122, 171.516
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein
IAA acetyltransferase


Mass: 17797.801 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Species: Bacillus cereus / Strain: ATCC 14579 / DSM 31 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q81FK8, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 3.61 Å3/Da / Density % sol: 65.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2.0 M Ammonium sulfate, CAPS pH 10.5 0.1 Lithium Sulfate, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97945 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jul 15, 2004
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.39→30.4 Å / Num. all: 37886 / Num. obs: 37374 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.115 / Net I/σ(I): 19.85
Reflection shellResolution: 2.39→2.39 Å / % possible all: 94.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
MAIDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.39→30.4 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / SU B: 13.123 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / σ(I): 0 / ESU R: 0.28 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23464 1869 5 %RANDOM
Rwork0.19841 ---
all0.20029 37374 --
obs0.20029 35505 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.246 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20.38 Å20 Å2
2--0.76 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 2.39→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4754 0 0 280 5034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224895
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9846587
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9565620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09423.596203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15215954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1851537
X-RAY DIFFRACTIONr_chiral_restr0.090.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023561
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.22013
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.23332
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5581.53147
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.96524901
X-RAY DIFFRACTIONr_scbond_it1.55731963
X-RAY DIFFRACTIONr_scangle_it2.554.51681
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 151 -
Rwork0.252 2601 -
obs--99.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.26960.2190.1512.01210.97420.8624-0.11860.1968-0.08870.0827-0.07580.1836-0.01020.02390.1944-0.043-0.09570.0424-0.0397-0.0663-0.06688.66258.9661.506
21.15620.0305-0.57680.4612-0.25370.95660.0744-0.05020.07610.0348-0.08660.082-0.05480.10340.0122-0.0851-0.03630.00860.0367-0.0222-0.070517.72145.085-27.898
31.7945-0.33540.64921.2218-0.13060.7640.0405-0.02070.11180.1217-0.2058-0.14920.0138-0.03990.1653-0.1127-0.0614-0.03710.03570.0728-0.0637-20.3242.236-27.212
41.02010.3943-0.46950.8555-0.50291.0824-0.05610.09960.10140.04410.03870.01240.0363-0.08670.0174-0.0119-0.0728-0.0169-0.04570.0114-0.0759-12.82227.4212.208
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1514 - 153
2X-RAY DIFFRACTION2BB2 - 1514 - 153
3X-RAY DIFFRACTION3CC2 - 1514 - 153
4X-RAY DIFFRACTION4DD2 - 1514 - 153

+
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