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- PDB-7v52: Structure of AdaV -

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Basic information

Entry
Database: PDB / ID: 7v52
TitleStructure of AdaV
ComponentsAdaV
KeywordsOXIDOREDUCTASE / Halogenase
Function / homology
Function and homology information


antibiotic biosynthetic process / metal ion binding
Similarity search - Function
B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Isopenicillin N synthase-like Fe(2+) 2OG dioxygenase domain-containing protein
Similarity search - Component
Biological speciesActinomadura sp. ATCC 39365 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.38 Å
AuthorsZhang, Z.Y. / Chen, W.Q. / Zhai, G.Q. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2018YFA0903200 China
CitationJournal: Acs Catalysis / Year: 2022
Title: Structural Insight into the Catalytic Mechanism of Non-Heme Iron Halogenase AdaV in 2'-Chloropentostatin Biosynthesis
Authors: Zhai, G.Q. / Gong, R. / Lin, Y. / Zhang, M. / Li, J. / Deng, Z. / Sun, J. / Chen, W. / Zhang, Z.G.
History
DepositionAug 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.nonpolymer_details
Revision 1.2Mar 1, 2023Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AdaV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0762
Polymers36,0201
Non-polymers561
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area11540 Å2
Unit cell
Length a, b, c (Å)139.980, 139.980, 48.204
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-516-

HOH

21A-603-

HOH

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Components

#1: Protein AdaV


Mass: 36019.789 Da / Num. of mol.: 1 / Mutation: G196E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomadura sp. ATCC 39365 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U8X168
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Nonpolymer detailsThe authors conducted crystallization experiments under aerobic conditions, and they were unable to ...The authors conducted crystallization experiments under aerobic conditions, and they were unable to confirm the valence state of FE in the structure.

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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: 3.78 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.085 M HEPES sodium pH 7.5, 1.7% v/v Polyethylene glycol 400, 1.7 M Ammonium sulfate, 15% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.38→19.93 Å / Num. obs: 21973 / % possible obs: 99.8 % / Redundancy: 19.6 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 26.2
Reflection shellResolution: 2.38→2.47 Å / Rmerge(I) obs: 0.858 / Num. unique obs: 2305

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.38→19.93 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2134 1056 4.81 %
Rwork0.2014 20895 -
obs0.202 21951 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.63 Å2 / Biso mean: 46.9384 Å2 / Biso min: 25.27 Å2
Refinement stepCycle: final / Resolution: 2.38→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 1 109 2131
Biso mean--68.11 49.36 -
Num. residues----267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.38-2.490.27151310.241525832714
2.49-2.620.28781100.221325882698
2.62-2.780.23651470.228225992746
2.78-30.25091250.215225902715
3-3.30.22761300.226326132743
3.3-3.770.19711120.196226252737
3.77-4.740.19281610.171626022763
4.74-19.930.19751400.198126952835

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