[English] 日本語
Yorodumi
- PDB-1z9u: Structural Genomics, The crystal structure of the acetyl transfer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1z9u
TitleStructural Genomics, The crystal structure of the acetyl transferase, modifies N-terminal serine of 50S ribosomal subunit protein L7/L12 from Salmonella typhimurium
Componentsacetyl transferase
KeywordsTRANSFERASE / acetyl transferase / L7/L12 / Salmonella typhimurium / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


peptide-alanine-alpha-N-acetyltransferase activity / peptide-serine-alpha-N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cytoplasm
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
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsZhang, R. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The crystal structure of the acetyl transferase, modifies N-terminal serine of 50S ribosomal subunit protein L7/L12 from Salmonella typhimurium
Authors: Zhang, R. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionApr 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: acetyl transferase
B: acetyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,02910
Polymers41,2612
Non-polymers7698
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: acetyl transferase
hetero molecules

B: acetyl transferase
hetero molecules

A: acetyl transferase
hetero molecules

A: acetyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,05920
Polymers82,5224
Non-polymers1,53716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
crystal symmetry operation6_664x-y+1,x+1,z-1/61
crystal symmetry operation8_665x-y+1,-y+1,-z1
Buried area8270 Å2
ΔGint-292 kcal/mol
Surface area32580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.700, 86.700, 237.996
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThis protein existed as dimer. MolA and MolB represent the dimer in the assymetric unit.

-
Components

#1: Protein acetyl transferase


Mass: 20630.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: GI:16764955 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q8ZPC0, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.186 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0M Ammonium sulphate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9797, 0.94656
DetectorType: SBC-2 / Detector: CCD / Date: Feb 5, 2004 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.946561
ReflectionResolution: 2.2→50 Å / Num. all: 26396 / Num. obs: 26286 / % possible obs: 99.58 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Biso Wilson estimate: 48.87 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 32.55
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3 / Num. unique all: 2544 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→29.5 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 10.067 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.198
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25673 1394 5 %RANDOM
Rwork0.21706 ---
all0.21903 26396 --
obs0.21903 26286 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.13 Å20 Å2
2--0.25 Å20 Å2
3----0.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2813 0 40 249 3102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212901
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9433922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0655344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01924.013152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68215503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8261522
X-RAY DIFFRACTIONr_chiral_restr0.0940.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022198
X-RAY DIFFRACTIONr_nbd_refined0.2050.21292
X-RAY DIFFRACTIONr_nbtor_refined0.30.21912
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2250
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.226
X-RAY DIFFRACTIONr_mcbond_it0.6371.51805
X-RAY DIFFRACTIONr_mcangle_it1.01722764
X-RAY DIFFRACTIONr_scbond_it1.52931280
X-RAY DIFFRACTIONr_scangle_it2.2934.51158
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 110 -
Rwork0.277 1827 -
obs--97.39 %
Refinement TLS params.Method: refined / Origin x: -15.845 Å / Origin y: 49.729 Å / Origin z: 6.516 Å
111213212223313233
T-0.1758 Å2-0.0086 Å20.0347 Å2--0.0809 Å2-0.0258 Å2---0.269 Å2
L2.9185 °21.2028 °2-0.9229 °2-1.0209 °2-0.3241 °2--1.4219 °2
S0.2405 Å °-0.1579 Å °0.2773 Å °0.1472 Å °-0.1151 Å °0.1256 Å °-0.2712 Å °0.0394 Å °-0.1254 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 403 - 40
2X-RAY DIFFRACTION1AA43 - 10043 - 100
3X-RAY DIFFRACTION1AA101 - 175101 - 175
4X-RAY DIFFRACTION1BB2 - 402 - 40
5X-RAY DIFFRACTION1BB41 - 10041 - 100
6X-RAY DIFFRACTION1BB101 - 175101 - 175

+
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://pdbjlvh1.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