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- PDB-8dle: Crosslinked Crystal Structure of the 8-amino-7-oxonanoate synthas... -

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Basic information

Entry
Database: PDB / ID: 8dle
TitleCrosslinked Crystal Structure of the 8-amino-7-oxonanoate synthase, BioF, and Benzene Sulfonyl Fluoride-crypto Acyl Carrier Protein, BSF-ACP
Components
  • 8-amino-7-oxononanoate synthase
  • Acyl carrier protein
KeywordsTRANSFERASE / BioF / AONS / crosslinking / ACP / complex / PLP
Function / homology
Function and homology information


8-amino-7-oxononanoate synthase / 8-amino-7-oxononanoate synthase activity / biotin biosynthetic process / acyl carrier activity / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
8-amino-7-oxononanoate synthase, Proteobacteria / 8-amino-7-oxononanoate synthase, Archaea/Proteobacteria type / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site ...8-amino-7-oxononanoate synthase, Proteobacteria / 8-amino-7-oxononanoate synthase, Archaea/Proteobacteria type / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Chem-SWC / Acyl carrier protein / 8-amino-7-oxononanoate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChen, A. / Davis, T.D. / Louie, G.V. / Bowman, M.E. / Noel, J.P. / Burkart, M.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095970 United States
CitationJournal: To Be Published
Title: Crosslinked Crystal Structure of the 8-amino-7-oxonanoate synthase, BioF, and Benzene Sulfonyl Fluoride-crypto Acyl Carrier Protein, BSF-ACP.
Authors: Chen, A. / Davis, T.D. / Re, R.N. / Louie, G.V. / Bowman, M.E. / Tran, K. / Clarke, D.J. / MacKay, C.L. / Campopiano, D.J. / Noel, J.P. / Burkart, M.D.
History
DepositionJul 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 8-amino-7-oxononanoate synthase
B: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5759
Polymers51,3582
Non-polymers1,2177
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.490, 162.310, 70.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-529-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein 8-amino-7-oxononanoate synthase / / AONS / 7-keto-8-amino-pelargonic acid synthase / 7-KAP synthase / KAPA synthase / 8-amino-7- ...AONS / 7-keto-8-amino-pelargonic acid synthase / 7-KAP synthase / KAPA synthase / 8-amino-7-ketopelargonate synthase


Mass: 42712.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bioF, bioF_1, bioF_2 / Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: J7QD78, 8-amino-7-oxononanoate synthase
#2: Protein Acyl carrier protein / / ACP


Mass: 8645.460 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B7MJ81

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Non-polymers , 5 types, 97 molecules

#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-SWC / N-{(2R)-2-hydroxy-3,3-dimethyl-4-[(trihydroxy-lambda~5~-phosphanyl)oxy]butanoyl}-beta-alanyl-N-(2-{4-[fluoro(dihydroxy)-lambda~4~-sulfanyl]phenyl}ethyl)-beta-alaninamide


Mass: 557.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H33FN3O10PS
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→53.57 Å / Num. obs: 20184 / % possible obs: 81.05 % / Redundancy: 1.8598 % / Biso Wilson estimate: 33.94 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.08077 / Rpim(I) all: 0.08077 / Rrim(I) all: 0.1142 / Net I/σ(I): 7.37
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 1.8586 % / Rmerge(I) obs: 0.7681 / Mean I/σ(I) obs: 0.47 / Num. unique obs: 1669 / CC1/2: 0.316 / CC star: 0.693 / Rpim(I) all: 0.7681 / Rrim(I) all: 1.086 / % possible all: 69.26

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BS0, 2FAD

1bs0

2fad


Resolution: 2.3→53.57 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 1045 5.23 %
Rwork0.2031 18945 -
obs0.2053 19990 81.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.78 Å2 / Biso mean: 56.6519 Å2 / Biso min: 16.15 Å2
Refinement stepCycle: final / Resolution: 2.3→53.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 73 90 3660
Biso mean--85.26 35.9 -
Num. residues----457
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.420.32531210.32442289241070
2.42-2.570.3251540.2972289244370
2.57-2.770.32831290.27012377250672
2.77-3.050.34781210.25392347246871
3.05-3.490.23221430.20952820296384
3.49-4.40.22511750.161633553530100
4.4-53.570.19422020.16653468367099
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)
10.30110.3707-0.57652.2115-1.72071.66080.0196-0.30380.10020.4265-0.1116-0.3876-0.25490.4790.13070.3498-0.0769-0.04550.3737-0.00360.257420.49821.6743-11.844
21.2018-0.23580.28421.563-0.08781.4471-0.0817-0.09210.19390.1354-0.02680.0386-0.1654-0.03730.09380.1634-0.01730.01760.1899-0.03410.1954-6.236923.1424-5.0664
32.2125-0.3222-0.11321.13950.64591.521-0.2736-0.42930.72690.36310.3063-0.4079-0.03810.48230.05820.4266-0.0471-0.1230.5848-0.05210.433417.585419.02317.0888
42.28880.1335-0.11890.4717-0.73321.14280.2494-0.01690.3204-0.12790.1033-0.5099-0.51690.2018-0.36450.6861-0.00470.08930.6767-0.05781.5678-5.924259.4143-41.7538
51.82151.0057-0.2750.5589-0.23923.34690.16820.03480.8073-0.24830.1689-0.1348-0.9663-0.4544-0.31981.24350.4486-0.07891.06380.10541.6821-13.070159.9877-49.6864
64.3681.3818-0.12673.17044.24926.73460.48540.45660.3662-0.40510.0536-0.7074-0.5337-0.0334-0.32520.4370.18-0.05660.57720.05720.9311-18.149954.6598-42.0051
72.7476-3.1424-0.11323.7241-0.36262.16870.12450.1198-0.14210.15250.0451-0.330.05190.0203-0.13120.72420.2131-0.43260.6658-0.05721.4224-8.242946.5458-39.24
80.7449-1.14920.91831.7882-1.42781.14310.1617-0.03660.14560.3025-0.0072-0.3907-0.12880.0006-0.16310.6401-0.0935-0.3331.0361-0.00081.6302-0.536851.7087-33.2979
90.2464-0.0149-0.55020.0149-0.0031.32010.1726-0.7996-0.61491.0491-0.0637-0.73710.60350.3081-0.18461.0730.0637-0.11510.86820.16870.9775-13.256349.3088-29.5682
104.22110.1486-0.88922.9560.4990.29610.1992-0.3253-0.0680.7683-0.0946-0.77280.0290.3525-0.16430.94410.1694-0.39220.7282-0.28081.2185-8.463359.0313-30.2725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 42 )A2 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 307 )A43 - 307
3X-RAY DIFFRACTION3chain 'A' and (resid 308 through 382 )A308 - 382
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 15 )B1 - 15
5X-RAY DIFFRACTION5chain 'B' and (resid 16 through 20 )B16 - 20
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 35 )B21 - 35
7X-RAY DIFFRACTION7chain 'B' and (resid 36 through 46 )B36 - 46
8X-RAY DIFFRACTION8chain 'B' and (resid 47 through 55 )B47 - 55
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 64 )B56 - 64
10X-RAY DIFFRACTION10chain 'B' and (resid 65 through 76 )B65 - 76

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