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- PDB-7v7x: Structure of H194A AdaV -

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Basic information

Entry
Database: PDB / ID: 7v7x
TitleStructure of H194A 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'-DEOXYADENOSINE-5'-MONOPHOSPHATE / 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: 2.7 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 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 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)36,2122
Polymers35,8811
Non-polymers3311
Water70339
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint2 kcal/mol
Surface area12200 Å2
Unit cell
Length a, b, c (Å)140.311, 140.311, 48.322
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-533-

HOH

21A-534-

HOH

31A-539-

HOH

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Components

#1: Protein AdaV


Mass: 35880.656 Da / Num. of mol.: 1 / Mutation: H194A
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-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE


Mass: 331.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.83 Å3/Da / Density % sol: 67.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.085 M HEPSE sodium pH7.5 1.7% 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: 2.6→19.98 Å / Num. obs: 17011 / % possible obs: 99.8 % / Redundancy: 20 % / CC1/2: 0.999 / Net I/σ(I): 26.3
Reflection shellResolution: 2.6→2.72 Å / Num. unique obs: 2049 / CC1/2: 0.951

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Processing

Software
NameVersionClassification
PHENIXv1.0refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→19.98 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.005 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 789 5.2 %RANDOM
Rwork0.1887 ---
obs0.191 14388 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 202.92 Å2 / Biso mean: 52.707 Å2 / Biso min: 29.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å2-0 Å2
2---0.01 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 2.7→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 22 39 2162
Biso mean--161.77 49.28 -
Num. residues----276
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 57 -
Rwork0.268 1018 -
all-1075 -
obs--99.91 %

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