[English] 日本語
Yorodumi
- PDB-6itd: Crystal structure of BioU (K124A) from Synechocystis sp.PCC6803 i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6itd
TitleCrystal structure of BioU (K124A) from Synechocystis sp.PCC6803 in complex with the analog of reaction intermediate, 3-(1-aminoethyl)-nonanedioic acid
ComponentsSlr0355 protein
KeywordsOXIDOREDUCTASE / BioU / biotin biosynthesis / Synechocystis
Function / homology
Function and homology information


8-amino-7-oxononanoate carboxylating dehydrogenase / biotin biosynthetic process / amino acid metabolic process / transaminase activity / NAD binding / NADP binding / oxidoreductase activity
Similarity search - Function
(S)-8-amino-7-oxononanoate synthase BioU-like / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
3-(1-AMINOETHYL)NONANEDIOIC ACID / (S)-8-amino-7-oxononanoate synthase BioU
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSakaki, K. / Tomita, T. / Kuzuyama, T. / Nishiyama, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science Japan
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria.
Authors: Sakaki, K. / Ohishi, K. / Shimizu, T. / Kobayashi, I. / Mori, N. / Matsuda, K. / Tomita, T. / Watanabe, H. / Tanaka, K. / Kuzuyama, T. / Nishiyama, M.
History
DepositionNov 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 8, 2020Group: 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 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Slr0355 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0262
Polymers37,7951
Non-polymers2311
Water88349
1
A: Slr0355 protein
hetero molecules

A: Slr0355 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0524
Polymers75,5902
Non-polymers4632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area5400 Å2
ΔGint-17 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.167, 71.167, 98.211
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-542-

HOH

21A-545-

HOH

-
Components

#1: Protein Slr0355 protein / BioU


Mass: 37794.789 Da / Num. of mol.: 1 / Mutation: K124A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: slr0355 / Production host: Escherichia coli (E. coli) / References: UniProt: Q55650
#2: Chemical ChemComp-IKT / 3-(1-AMINOETHYL)NONANEDIOIC ACID


Mass: 231.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H21NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.9 Å3/Da / Density % sol: 35.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% (w/v) polyethylene glycol 3350, 0.2 M ammonium acetate, 5mM 3-(1-aminoethyl)-nonanedioic acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→61.63 Å / Num. obs: 19876 / % possible obs: 99.9 % / Redundancy: 8.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.035 / Net I/σ(I): 31.9
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.588 / Num. unique obs: 981 / CC1/2: 0.973 / Rpim(I) all: 0.203

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IR4

6ir4


Resolution: 2→61.63 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.067 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.185 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24883 959 4.8 %RANDOM
Rwork0.18749 ---
obs0.19033 18887 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.195 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2→61.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 16 49 2520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192511
X-RAY DIFFRACTIONr_bond_other_d0.0020.022424
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9583398
X-RAY DIFFRACTIONr_angle_other_deg0.8483.0035562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7465327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3624.766107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7615411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.171513
X-RAY DIFFRACTIONr_chiral_restr0.0730.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022895
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02558
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
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_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3684.5371311
X-RAY DIFFRACTIONr_mcbond_other2.3684.5371310
X-RAY DIFFRACTIONr_mcangle_it3.3646.7931637
X-RAY DIFFRACTIONr_mcangle_other3.3636.7931638
X-RAY DIFFRACTIONr_scbond_it3.1245.0991200
X-RAY DIFFRACTIONr_scbond_other3.125.11198
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0127.4741761
X-RAY DIFFRACTIONr_long_range_B_refined6.55636.7632760
X-RAY DIFFRACTIONr_long_range_B_other6.55236.7432748
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.004→2.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 55 -
Rwork0.246 1393 -
obs--99.45 %

+
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