[English] 日本語
Yorodumi
- PDB-5c82: Crystal structure of Nourseothricin acetyltransferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c82
TitleCrystal structure of Nourseothricin acetyltransferase
ComponentsNourseothricin acetyltransferase
KeywordsTRANSFERASE / Acettyl transferase / antibiotic ressistance / Se-Met SAD
Function / homology
Function and homology information


N-acetyltransferase activity
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
D(-)-TARTARIC ACID / Nourseothricin acetyltransferase
Similarity search - Component
Biological speciesStreptomyces noursei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKumar, D. / Ghosh, A. / Taneja, B. / Chakraborty, K.
Funding support India, 1items
OrganizationGrant numberCountry
CSIR-IGIB India
CitationJournal: To Be Published
Title: Crystal structure of Nourseothricin acetyltransferase
Authors: Kumar, D. / Ghosh, A. / Taneja, B. / Chakraborty, K.
History
DepositionJun 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 4, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: citation / diffrn_source ...citation / diffrn_source / entity_poly / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_beamline ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _entity_poly.pdbx_target_identifier / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nourseothricin acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9412
Polymers20,7911
Non-polymers1501
Water1,74797
1
A: Nourseothricin acetyltransferase
hetero molecules

A: Nourseothricin acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8824
Polymers41,5822
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2720 Å2
ΔGint-8 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.536, 44.641, 42.244
Angle α, β, γ (deg.)90.00, 97.67, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Nourseothricin acetyltransferase


Mass: 20790.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces noursei (bacteria) / Gene: nat1 / Plasmid: pET-SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) ROSETTA / References: UniProt: Q08414
#2: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.75 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 297.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1 M Buffer ...Details: 0.1 M Carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1 M Buffer System 3(Tris base; BICINE) 8.5, 50 % v/v Precipitant Mix 4(25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97869 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 9, 2015
RadiationMonochromator: Si (111) and Si (220) Double crystal monochromato
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 2.2→33.82 Å / Num. obs: 9075 / % possible obs: 98.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 29.45 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 21.4
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.341 / % possible all: 90.8

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→15.28 Å / Cor.coef. Fo:Fc: 0.9328 / Cor.coef. Fo:Fc free: 0.9031 / SU R Cruickshank DPI: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.269 / SU Rfree Blow DPI: 0.196 / SU Rfree Cruickshank DPI: 0.195
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 465 5.14 %RANDOM
Rwork0.1807 ---
obs0.1829 9046 98.69 %-
Displacement parametersBiso mean: 29.43 Å2
Baniso -1Baniso -2Baniso -3
1-6.3899 Å20 Å22.5328 Å2
2---1.7618 Å20 Å2
3----4.6281 Å2
Refine analyzeLuzzati coordinate error obs: 0.269 Å
Refinement stepCycle: 1 / Resolution: 2.2→15.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1306 0 10 97 1413
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011347HARMONIC2
X-RAY DIFFRACTIONt_angle_deg11837HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d440SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes30HARMONIC2
X-RAY DIFFRACTIONt_gen_planes208HARMONIC5
X-RAY DIFFRACTIONt_it1347HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion19.5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion174SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1591SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.46 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2532 126 5.12 %
Rwork0.1852 2334 -
all0.1886 2460 -
obs--95.34 %

+
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