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- PDB-7jsd: Hydroxylase homolog of BesD with Fe(II), alpha-ketoglutarate, and... -

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Basic information

Entry
Database: PDB / ID: 7jsd
TitleHydroxylase homolog of BesD with Fe(II), alpha-ketoglutarate, and lysine
ComponentsLysine hydroxylase
KeywordsBIOSYNTHETIC PROTEIN / Hydroxylase / non-heme iron
Function / homologyq2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta / 2-OXOGLUTARIC ACID / : / LYSINE
Function and homology information
Biological speciesStreptomyces roseifaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKissman, E.N. / Neugebauer, M.E. / Chang, M.C.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)LBNL DEAC02-05CH11231, FWP CH030201 United States
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Reaction pathway engineering converts a radical hydroxylase into a halogenase.
Authors: Neugebauer, M.E. / Kissman, E.N. / Marchand, J.A. / Pelton, J.G. / Sambold, N.A. / Millar, D.C. / Chang, M.C.Y.
History
DepositionAug 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: 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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Lysine hydroxylase
B: Lysine hydroxylase
C: Lysine hydroxylase
D: Lysine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,95317
Polymers120,3154
Non-polymers1,63813
Water7,260403
1
A: Lysine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6225
Polymers30,0791
Non-polymers5434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6225
Polymers30,0791
Non-polymers5434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4284
Polymers30,0791
Non-polymers3493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2813
Polymers30,0791
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.626, 93.530, 91.339
Angle α, β, γ (deg.)90.000, 107.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Lysine hydroxylase


Mass: 30078.697 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces roseifaciens (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 416 molecules

#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: In an anaerobic chamber, equal volumes of protein solution (3 mg/mL Hydroxylase, lysine (3 mM), KG (3 mM, pH 7)) and reservoir solution (HEPES pH 7.0 (100 mM), sodium nitrate (200 mM) ...Details: In an anaerobic chamber, equal volumes of protein solution (3 mg/mL Hydroxylase, lysine (3 mM), KG (3 mM, pH 7)) and reservoir solution (HEPES pH 7.0 (100 mM), sodium nitrate (200 mM) containing 28% (w/v) PEG 3350); Crystals were soaked with iron chloride before flash freezing

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Data collection

DiffractionMean temperature: 194 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.111 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.111 Å / Relative weight: 1
ReflectionResolution: 2.5→87.081 Å / Num. obs: 40203 / % possible obs: 99.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 38.69 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.253 / Rrim(I) all: 0.2744 / Net I/σ(I): 6.2
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 1.644 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 3972 / CC1/2: 0.519 / CC star: 0.827

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NIE

6nie


Resolution: 2.5→87.08 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 1967 4.89 %
Rwork0.1802 38233 -
obs0.1826 40200 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.85 Å2 / Biso mean: 43.7164 Å2 / Biso min: 13.89 Å2
Refinement stepCycle: final / Resolution: 2.5→87.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7831 0 100 403 8334
Biso mean--43.56 43.84 -
Num. residues----989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0018110
X-RAY DIFFRACTIONf_angle_d0.43411021
X-RAY DIFFRACTIONf_dihedral_angle_d13.234834
X-RAY DIFFRACTIONf_chiral_restr0.0411237
X-RAY DIFFRACTIONf_plane_restr0.0031438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.56260.30461290.2546270799
2.5626-2.63190.32031390.2445269199
2.6319-2.70930.30521260.2355272899
2.7093-2.79680.30481320.2323271699
2.7968-2.89670.3191470.2255273099
2.8967-3.01270.26461450.1961269599
3.0127-3.14980.26121280.20282742100
3.1498-3.31590.25081640.18942680100
3.3159-3.52370.24771440.1741272899
3.5237-3.79570.17681400.15762746100
3.7957-4.17770.19231370.14582734100
4.1777-4.78220.19531470.13532755100
4.7822-6.02480.20071480.17392762100
6.0248-87.080.19541410.18432819100

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