[English] 日本語
Yorodumi
- PDB-3lsc: Crystal structure of the mutant E241Q of atrazine chlorohydrolase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lsc
TitleCrystal structure of the mutant E241Q of atrazine chlorohydrolase TrzN from Arthrobacter aurescens TC1 complexed with zinc and atraton
ComponentsTriazine hydrolase
KeywordsHYDROLASE / atrazine chlorohydrolase TrzN / E241Q / atraton
Function / homology
Function and homology information


amidase activity / metal ion binding
Similarity search - Function
Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel ...Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-AOO / Triazine hydrolase
Similarity search - Component
Biological speciesArthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Seffernick, J. / Wackett, L.P. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of the mutant E241Q of atrazine chlorohydrolase TrzN from Arthrobacter aurescens TC1 complexed with zinc and atraton
Authors: Fedorov, A.A. / Fedorov, E.V. / Seffernick, J. / Wackett, L.P. / Almo, S.C.
History
DepositionFeb 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Triazine hydrolase
B: Triazine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0195
Polymers99,6772
Non-polymers3423
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-72 kcal/mol
Surface area28740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.378, 101.621, 80.767
Angle α, β, γ (deg.)90.00, 104.45, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Triazine hydrolase


Mass: 49838.668 Da / Num. of mol.: 2 / Fragment: UNP residues 14-469 / Mutation: E241Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter aurescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6SJY7
#2: Chemical ChemComp-AOO / N-ethyl-6-methoxy-N'-(1-methylethyl)-1,3,5-triazine-2,4-diamine / Atraton


Mass: 211.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17N5O
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG4000, 0.1M sodium citrate, 0.2M ammonium acetate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.64→40 Å / Num. obs: 108286 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.071

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LS9

3ls9


Resolution: 1.64→39.106 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 5408 4.99 %RANDOM
Rwork0.1893 ---
obs0.1906 108286 98.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.027 Å2 / ksol: 0.352 e/Å3
Refinement stepCycle: LAST / Resolution: 1.64→39.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6956 0 17 431 7404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067129
X-RAY DIFFRACTIONf_angle_d1.0299699
X-RAY DIFFRACTIONf_dihedral_angle_d15.8972581
X-RAY DIFFRACTIONf_chiral_restr0.0681080
X-RAY DIFFRACTIONf_plane_restr0.0041279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.65730.331190.28762628X-RAY DIFFRACTION76
1.6573-1.67680.27081750.28083067X-RAY DIFFRACTION88
1.6768-1.69730.33371670.26493366X-RAY DIFFRACTION96
1.6973-1.71870.28271820.253410X-RAY DIFFRACTION99
1.7187-1.74140.29941610.24653484X-RAY DIFFRACTION100
1.7414-1.76520.27991820.23593461X-RAY DIFFRACTION100
1.7652-1.79040.26541970.22273465X-RAY DIFFRACTION100
1.7904-1.81710.23431830.21823399X-RAY DIFFRACTION100
1.8171-1.84550.25742030.2123501X-RAY DIFFRACTION100
1.8455-1.87580.26121950.20763454X-RAY DIFFRACTION100
1.8758-1.90810.24081820.21033459X-RAY DIFFRACTION100
1.9081-1.94280.26091720.20423467X-RAY DIFFRACTION100
1.9428-1.98020.24591740.19153487X-RAY DIFFRACTION100
1.9802-2.02060.21791580.19073490X-RAY DIFFRACTION100
2.0206-2.06460.22381730.18353492X-RAY DIFFRACTION100
2.0646-2.11260.21521820.18443481X-RAY DIFFRACTION100
2.1126-2.16540.211930.18043451X-RAY DIFFRACTION100
2.1654-2.2240.21411860.18683456X-RAY DIFFRACTION100
2.224-2.28940.21241420.18793535X-RAY DIFFRACTION100
2.2894-2.36330.21651950.18153433X-RAY DIFFRACTION100
2.3633-2.44770.20411870.18893482X-RAY DIFFRACTION100
2.4477-2.54570.22691950.19143466X-RAY DIFFRACTION100
2.5457-2.66150.23152130.19193443X-RAY DIFFRACTION100
2.6615-2.80180.22891910.19773467X-RAY DIFFRACTION100
2.8018-2.97730.20441830.19453496X-RAY DIFFRACTION100
2.9773-3.20710.2212000.20193469X-RAY DIFFRACTION100
3.2071-3.52970.19651910.18993487X-RAY DIFFRACTION100
3.5297-4.040.18361560.15913527X-RAY DIFFRACTION100
4.04-5.08820.15891920.14363508X-RAY DIFFRACTION100
5.0882-39.11710.17471790.16833547X-RAY DIFFRACTION99

+
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