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- PDB-7w5s: A nonheme iron- and alpha-ketoglutarate- dependent halogenase tha... -

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Basic information

Entry
Database: PDB / ID: 7w5s
TitleA nonheme iron- and alpha-ketoglutarate- dependent halogenase that catalyzes nucleotide substrates
Componentsnonheme iron and alpha-ketoglutarate dependent halogenase
KeywordsTRANSFERASE / 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
: / DI(HYDROXYETHYL)ETHER / Isopenicillin N synthase-like Fe(2+) 2OG dioxygenase domain-containing protein
Similarity search - Component
Biological speciesActinomadura sp. ATCC 39365 (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.76 Å
AuthorsDai, L.H. / Zhang, X. / Hu, Y.M. / Huang, J.W. / Chen, C.C. / Guo, R.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Appl.Environ.Microbiol. / Year: 2022
Title: Structural and Functional Insights into a Nonheme Iron- and alpha-Ketoglutarate-Dependent Halogenase That Catalyzes Chlorination of Nucleotide Substrates.
Authors: Dai, L. / Zhang, X. / Hu, Y. / Shen, J. / Zhang, Q. / Zhang, L. / Min, J. / Chen, C.C. / Liu, Y. / Huang, J.W. / Guo, R.T.
History
DepositionNov 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 25, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
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: nonheme iron and alpha-ketoglutarate dependent halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,53913
Polymers34,4171
Non-polymers1,12212
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-26 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.492, 72.330, 81.117
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein nonheme iron and alpha-ketoglutarate dependent halogenase


Mass: 34417.012 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

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Non-polymers , 5 types, 371 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Ammonium Sulfate, HEPES pH 7.5, PEG 400, di-Potassium hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Dec 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.76→37.63 Å / Num. obs: 31366 / % possible obs: 99.8 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.5
Reflection shellResolution: 1.76→1.79 Å / Rmerge(I) obs: 0.193 / Num. unique obs: 1516

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SADABSdata scaling
PDB_EXTRACT3.27data extraction
SAINTdata reduction
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 1.76→32.09 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.354 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1815 1546 5 %RANDOM
Rwork0.1485 ---
obs0.1502 29286 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65 Å2 / Biso mean: 14.608 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.82 Å2-0 Å2-0 Å2
2---4.13 Å2-0 Å2
3---9.96 Å2
Refinement stepCycle: final / Resolution: 1.76→32.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 66 359 2736
Biso mean--34.95 26.45 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132444
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172248
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.6383307
X-RAY DIFFRACTIONr_angle_other_deg1.5111.5685201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7395305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.01421.016128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84715368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.331520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022743
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02521
LS refinement shellResolution: 1.76→1.805 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 89 -
Rwork0.162 1781 -
all-1870 -
obs--82.6 %

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