[English] 日本語
Yorodumi
- PDB-5yum: Crystallographic structures of IlvN.Val/Ile complexes:Conformatio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yum
TitleCrystallographic structures of IlvN.Val/Ile complexes:Conformational selectivity for feedback inhibition of AHASs
ComponentsAcetolactate synthase isozyme 1 small subunit
KeywordsTRANSFERASE / Transferase subunit / Regulatory subunit / ACT protein / amino acid binding
Function / homology
Function and homology information


acetolactate synthase regulator activity / acetolactate synthase / acetolactate synthase complex / branched-chain amino acid biosynthetic process / acetolactate synthase activity / valine biosynthetic process / isoleucine biosynthetic process / cytosol
Similarity search - Function
Acetolactate synthase, small subunit / AHAS, ACT domain / ACT domain / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / ISOLEUCINE / Acetolactate synthase isozyme 1 small subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.432 Å
AuthorsSarma, S.P. / Bansal, A. / Schindelin, H. / Demeler, B.
Funding support India, 1items
OrganizationGrant numberCountry
DSTO1544 India
Citation
Journal: Biochemistry / Year: 2019
Title: Crystallographic Structures of IlvN·Val/Ile Complexes: Conformational Selectivity for Feedback Inhibition of Aceto Hydroxy Acid Synthases.
Authors: Bansal, A. / Karanth, N.M. / Demeler, B. / Schindelin, H. / Sarma, S.P.
#1: Journal: Biochemistry / Year: 2013
Title: The coil-to-helix transition in IlvN regulates the allosteric control of Escherichia coli acetohydroxyacid synthase I.
Authors: Karanth, N.M. / Sarma, S.P.
#2: Journal: Biochemistry / Year: 2008
Title: Escherichia coli ilvN interacts with the FAD binding domain of ilvB and activates the AHAS I enzyme.
Authors: Mitra, A. / Sarma, S.P.
History
DepositionNov 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetolactate synthase isozyme 1 small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4533
Polymers11,2631
Non-polymers1902
Water46826
1
A: Acetolactate synthase isozyme 1 small subunit
hetero molecules

A: Acetolactate synthase isozyme 1 small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9066
Polymers22,5262
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area2500 Å2
ΔGint-19 kcal/mol
Surface area9190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.620, 89.620, 86.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-102-

CO

-
Components

#1: Protein Acetolactate synthase isozyme 1 small subunit / Acetohydroxy-acid synthase I small subunit / ALS-I


Mass: 11262.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ilvN, b3670, JW3645 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADF8, acetolactate synthase
#2: Chemical ChemComp-ILE / ISOLEUCINE / Isoleucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 288 K / Method: microbatch / pH: 6.5
Details: 0.01M cobalt(II) chloride hexahydrate, 0.1M MES monohydrate pH 6.5, 1.8M ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.43→57.88 Å / Num. obs: 5202 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.031 / Rrim(I) all: 0.075 / Net I/σ(I): 20.7
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 534 / CC1/2: 0.949 / Rpim(I) all: 0.195 / Rrim(I) all: 0.037 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIXv1.13-2998-000refinement
iMOSFLMv7.0data reduction
Aimlessv7.0data scaling
PHASERv7.0phasing
REFMACv7.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LVW
Resolution: 2.432→57.878 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.69
RfactorNum. reflection% reflection
Rfree0.2261 353 6.81 %
Rwork0.191 --
obs0.1936 5187 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.432→57.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms727 0 10 26 763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003752
X-RAY DIFFRACTIONf_angle_d0.6211022
X-RAY DIFFRACTIONf_dihedral_angle_d7.981631
X-RAY DIFFRACTIONf_chiral_restr0.046120
X-RAY DIFFRACTIONf_plane_restr0.004135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4323-2.78430.29311170.21451580X-RAY DIFFRACTION100
2.7843-3.50780.26211040.20691614X-RAY DIFFRACTION100
3.5078-57.89430.19951320.17671640X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -3.862 Å / Origin y: 22.5038 Å / Origin z: 1.109 Å
111213212223313233
T0.249 Å2-0.0019 Å20.006 Å2-0.2831 Å2-0.0013 Å2--0.3432 Å2
L5.4458 °2-0.7097 °2-0.1742 °2-6.4943 °2-0.1352 °2--6.2998 °2
S-0.2885 Å °-0.2545 Å °0.128 Å °-0.2611 Å °0.0401 Å °-0.5522 Å °-0.3746 Å °0.5986 Å °0.1933 Å °
Refinement TLS groupSelection details: all

+
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