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- PDB-6kue: The structure of BioZ from Agrobacterium tumefaciens -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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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.

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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

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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

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