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- PDB-7w5t: A nonheme iron- and alpha-ketoglutarate- dependent halogenase tha... -

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Basic information

Entry
Database: PDB / ID: 7w5t
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
2-OXOGLUTARIC ACID / : / 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 / MOLECULAR REPLACEMENT / Resolution: 1.74 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 1.3Nov 29, 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

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Assembly

Deposited unit
A: nonheme iron and alpha-ketoglutarate dependent halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0598
Polymers34,4171
Non-polymers6427
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-20 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.649, 71.255, 82.473
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 , 6 types, 311 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / 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: 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
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.25 Å3/Da / Density % sol: 45.27 %
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 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.74→32.71 Å / Num. obs: 32596 / % possible obs: 99.2 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.2
Reflection shellResolution: 1.74→1.77 Å / Rmerge(I) obs: 0.262 / Num. unique obs: 1599

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Processing

Software
NameVersionClassification
SADABSdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7W5S

7w5s


Resolution: 1.74→32.71 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.409 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / 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
Rfree0.189 1601 5 %RANDOM
Rwork0.1579 ---
obs0.1595 30623 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.53 Å2 / Biso mean: 18.359 Å2 / Biso min: 1.06 Å2
Baniso -1Baniso -2Baniso -3
1--4.61 Å2-0 Å2-0 Å2
2---5 Å2-0 Å2
3---9.61 Å2
Refinement stepCycle: final / Resolution: 1.74→32.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 36 304 2551
Biso mean--34.35 31.06 -
Num. residues----289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132306
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172107
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.643129
X-RAY DIFFRACTIONr_angle_other_deg1.5231.5714868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4965289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.93320.738122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34615348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7041519
X-RAY DIFFRACTIONr_chiral_restr0.090.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022614
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02503
LS refinement shellResolution: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 89 -
Rwork0.184 2064 -
all-2153 -
obs--90.69 %

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