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- PDB-7v57: Structure of AdaV -

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Basic information

Entry
Database: PDB / ID: 7v57
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
2-OXOGLUTARIC ACID / : / 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: 2.35 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 1.1Mar 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 1.2May 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)36,1854
Polymers35,9481
Non-polymers2373
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-25 kcal/mol
Surface area11390 Å2
Unit cell
Length a, b, c (Å)139.450, 139.450, 48.103
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-504-

HOH

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Components

#1: Protein AdaV


Mass: 35947.727 Da / Num. of mol.: 1
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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
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: 3.76 Å3/Da / Density % sol: 67.25 %
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 PILATUS 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: 2.35→19.85 Å / Num. obs: 22606 / % possible obs: 99.8 % / Redundancy: 20 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 28.2
Reflection shellResolution: 2.35→2.44 Å / Rmerge(I) obs: 0.947 / Num. unique obs: 2359

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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: 2.35→19.85 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 1106 4.9 %
Rwork0.209 21469 -
obs0.2105 22575 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.55 Å2 / Biso mean: 51.7592 Å2 / Biso min: 30.27 Å2
Refinement stepCycle: final / Resolution: 2.35→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1998 0 12 65 2075
Biso mean--89.03 52.96 -
Num. residues----265
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
2.35-2.460.3141380.236526632801
2.46-2.590.22811490.210326502799
2.59-2.750.28081210.241526602781
2.75-2.960.27671190.220526942813
2.96-3.260.28541530.237726552808
3.26-3.720.22071310.20826892820
3.72-4.680.21221420.186426912833
4.68-19.850.22791530.204627672920

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