[English] 日本語
Yorodumi
- PDB-6kue: The structure of BioZ from Agrobacterium tumefaciens -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kue
TitleThe structure of BioZ from Agrobacterium tumefaciens
Components3-oxoacyl-[acyl-carrier-protein] synthase III
KeywordsTRANSFERASE / Structure BioZ
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase-like
Similarity search - Domain/homology
3-oxoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.992 Å
AuthorsOuyang, S. / Hongxin, G. / Sitao, Z.
CitationJournal: Nat Commun / Year: 2021
Title: Biochemical and structural characterization of the BioZ enzyme engaged in bacterial biotin synthesis pathway.
Authors: Zhang, S. / Xu, Y. / Guan, H. / Cui, T. / Liao, Y. / Wei, W. / Li, J. / Hassan, B.H. / Zhang, H. / Jia, X. / Ouyang, S. / Feng, Y.
History
DepositionSep 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Apr 21, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase III
B: 3-oxoacyl-[acyl-carrier-protein] synthase III


Theoretical massNumber of molelcules
Total (without water)68,2842
Polymers68,2842
Non-polymers00
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-43 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.810, 85.780, 110.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase III / BioZ


Mass: 34141.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: SY94_3983 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0F4FMM6, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 289.15 K / Method: counter-diffusion / Details: 0.2M Sodium nitate,20%PEG3,350.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→55.26 Å / Num. obs: 41976 / % possible obs: 99.46 % / Redundancy: 25.2 % / Biso Wilson estimate: 16.11 Å2 / Rmerge(I) obs: 0.371 / Net I/σ(I): 15.8
Reflection shellResolution: 1.99→2.063 Å / Rmerge(I) obs: 1.114 / Num. unique obs: 4100

-
Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.992→46.443 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 25.8
RfactorNum. reflection% reflection
Rfree0.2285 2037 4.86 %
Rwork0.181 --
obs0.1833 41943 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.63 Å2 / Biso mean: 20.8793 Å2 / Biso min: 5.01 Å2
Refinement stepCycle: final / Resolution: 1.992→46.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4764 0 0 423 5187
Biso mean---31.28 -
Num. residues----654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084830
X-RAY DIFFRACTIONf_angle_d0.9436556
X-RAY DIFFRACTIONf_chiral_restr0.058776
X-RAY DIFFRACTIONf_plane_restr0.005866
X-RAY DIFFRACTIONf_dihedral_angle_d5.6912918
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9921-2.03840.26641310.20782593100
2.0384-2.08940.24851350.19492625100
2.0894-2.14590.25941310.1927260199
2.1459-2.20910.25731350.19562643100
2.2091-2.28040.26981200.18772666100
2.2804-2.36190.24811470.19322601100
2.3619-2.45640.22431270.19122686100
2.4564-2.56820.24431320.1982612100
2.5682-2.70360.23911290.18772674100
2.7036-2.8730.25831440.19112643100
2.873-3.09470.22281500.1815260098
3.0947-3.40610.19891420.17312685100
3.4061-3.89870.23041310.16412722100
3.8987-4.91110.19011370.15222745100
4.9111-39.980.20591460.1837281098
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.20690.6320.54711.81030.93733.0888-0.0601-0.04140.1487-0.2032-0.0370.25990.0866-0.0057-0.04640.05350.016-0.03610.10070.04340.1352-18.298343.36654.2656
21.98231.5099-0.05862.88490.08081.3618-0.15060.15880.2653-0.47510.00070.43970.0699-0.18520.05580.1568-0.0278-0.06830.11920.02650.1484-22.13736.714843.8249
31.95520.1978-0.23361.76830.5552.3661-0.0440.08040.0707-0.04890.01870.0292-0.1560.01810.01240.0634-0.0006-0.00320.04880.0120.0841-6.030753.635158.5691
41.9728-0.404-0.88612.43740.73663.0665-0.036-0.0588-0.12330.1145-0.01220.03710.12130.01110.04490.02610.00230.00290.06250.01550.0565-3.088241.961367.5373
51.48010.73330.19671.21120.20442.0427-0.0550.1061-0.0474-0.10560.05430.05860.1230.1173-0.03380.08330.043-0.02520.0403-0.00430.1021-10.63342.347957.2763
61.76640.41630.01081.0225-0.25440.1458-0.0740.1707-0.1267-0.11220.0847-0.02280.0563-0.02970.00070.1069-0.0107-0.00370.0974-0.00360.09-6.815729.728455.7993
71.3245-0.27550.4871.93670.26051.0215-0.053-0.0395-0.0640.04960.02720.25140.1183-0.07790.02660.0628-0.01110.00570.09070.00950.1085-18.111534.685363.4397
80.93330.06250.34721.68520.39110.59510.0069-0.1551-0.0514-0.1845-0.0503-0.3991-0.2390.2652-0.06420.04550.02090.01910.0314-0.04720.184621.761441.999955.9376
93.21771.5737-0.16021.8043-0.29721.9584-0.22180.0696-0.1057-0.43370.2404-0.5283-0.17920.0567-0.00860.175-0.02490.10610.1388-0.02790.177426.368549.075444.2293
101.24190.2790.21891.1061-0.57641.8375-0.0289-0.0188-0.01990.00750.0083-0.02840.138-0.04080.02520.08430.02320.00940.0538-0.02170.099310.071332.092358.6671
111.8946-0.3093-0.03521.9691-1.12762.96290.0308-0.36980.20290.2363-0.1213-0.3134-0.1780.2560.0570.04190.0313-0.01690.0866-0.04610.11126.958343.744267.6135
120.91910.28320.8020.850.78081.2599-0.08110.25770.3234-0.27270.1979-0.0483-0.3046-0.0733-0.18950.12910.01450.05460.14240.06540.191714.751945.405349.1888
131.3093-0.05510.32491.25490.36960.1474-0.05880.25960.0971-0.20780.0509-0.0616-0.1980.0715-0.01730.1269-0.04040.04040.14820.00330.0847.644449.47453.9439
141.40070.4216-0.19382.4655-2.41442.62930.1932-0.10010.31610.15930.32070.0486-0.5796-0.3509-0.31460.11140.00340.00180.0941-0.030.172713.324861.772462.3605
151.3365-0.3218-0.04942.30270.33231.94390.0211-0.12460.18610.0602-0.0123-0.4667-0.14760.1633-0.0570.1009-0.0183-0.00420.1158-0.01490.217823.826455.441463.6272
162.2577-0.3494-0.50951.70870.10771.6555-0.0757-0.0592-0.06180.12150.0621-0.2012-0.06470.06060.05410.0653-0.0064-0.02870.0684-0.01970.133119.690247.473166.1524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 29 )A3 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 53 )A30 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 113 )A54 - 113
4X-RAY DIFFRACTION4chain 'A' and (resid 114 through 132 )A114 - 132
5X-RAY DIFFRACTION5chain 'A' and (resid 133 through 176 )A133 - 176
6X-RAY DIFFRACTION6chain 'A' and (resid 177 through 258 )A177 - 258
7X-RAY DIFFRACTION7chain 'A' and (resid 259 through 328 )A259 - 328
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 29 )B2 - 29
9X-RAY DIFFRACTION9chain 'B' and (resid 30 through 53 )B30 - 53
10X-RAY DIFFRACTION10chain 'B' and (resid 54 through 113 )B54 - 113
11X-RAY DIFFRACTION11chain 'B' and (resid 114 through 132 )B114 - 132
12X-RAY DIFFRACTION12chain 'B' and (resid 133 through 160 )B133 - 160
13X-RAY DIFFRACTION13chain 'B' and (resid 161 through 219 )B161 - 219
14X-RAY DIFFRACTION14chain 'B' and (resid 220 through 241 )B220 - 241
15X-RAY DIFFRACTION15chain 'B' and (resid 242 through 286 )B242 - 286
16X-RAY DIFFRACTION16chain 'B' and (resid 287 through 328 )B287 - 328

+
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