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- PDB-6nie: BesD with Fe(II), chloride, and alpha-ketoglutarate -

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Basic information

Entry
Database: PDB / ID: 6nie
TitleBesD with Fe(II), chloride, and alpha-ketoglutarate
ComponentsBesD, lysine halogenase
KeywordsBIOSYNTHETIC PROTEIN / halogenase
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and the other dehydrogenated / L-lysine 4-chlorinase activity / L-propargylglycine biosynthetic process / L-beta-ethynylserine biosynthetic process / antibiotic biosynthetic process
Similarity search - Function
2-OXOGLUTARIC ACID / : / : / LYSINE / L-lysine 4-chlorinase
Similarity search - Component
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsNeugebauer, M.E. / Chang, M.C.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: A family of radical halogenases for the engineering of amino-acid-based products.
Authors: Neugebauer, M.E. / Sumida, K.H. / Pelton, J.G. / McMurry, J.L. / Marchand, J.A. / Chang, M.C.Y.
History
DepositionDec 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BesD, lysine halogenase
B: BesD, lysine halogenase
C: BesD, lysine halogenase
D: BesD, lysine halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,87021
Polymers117,2764
Non-polymers1,59417
Water15,259847
1
A: BesD, lysine halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7045
Polymers29,3191
Non-polymers3854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BesD, lysine halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7596
Polymers29,3191
Non-polymers4405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BesD, lysine halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7045
Polymers29,3191
Non-polymers3854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BesD, lysine halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7045
Polymers29,3191
Non-polymers3854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.358, 68.916, 79.702
Angle α, β, γ (deg.)115.36, 91.57, 112.95
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
BesD, lysine halogenase


Mass: 29319.025 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cattleya (strain ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057) (bacteria)
Strain: ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057
Gene: SCATT_p06880 / Production host: Escherichia coli (E. coli) / References: UniProt: G8XHD5

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Non-polymers , 6 types, 864 molecules

#2: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 847 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1:1 volume of protein solution (10 mg/mL BesD, lysine (1.5 mM), alpha-ketoglutarate (3 mM, pH 7)) and reservoir solution (MES pH 6.5 (100 mM), sodium chloride (0.6 mM), containing 20% (v/v) ...Details: 1:1 volume of protein solution (10 mg/mL BesD, lysine (1.5 mM), alpha-ketoglutarate (3 mM, pH 7)) and reservoir solution (MES pH 6.5 (100 mM), sodium chloride (0.6 mM), containing 20% (v/v) PEG 4000. Soaked anaerobically in a solution containing (NH4)2Fe(SO4)2 * 6H2O (1mM), alpha-ketoglutarate (1 mM), sodium ascorbate (1 mM), lysine (1 mM), and glycerol (20% (v/v) for 30 min before flash freezing in liquid nitrogen

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Data collection

DiffractionMean temperature: 194 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.95→70.03 Å / Num. obs: 149915 / % possible obs: 97.35 % / Redundancy: 13.6 % / CC1/2: 0.998 / Net I/σ(I): 10.7
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 7341 / CC1/2: 0.78 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→70.027 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.68
RfactorNum. reflection% reflection
Rfree0.2159 7295 4.87 %
Rwork0.1772 --
obs0.1791 149912 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→70.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7808 0 89 847 8744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018118
X-RAY DIFFRACTIONf_angle_d0.98211065
X-RAY DIFFRACTIONf_dihedral_angle_d18.9772979
X-RAY DIFFRACTIONf_chiral_restr0.0581236
X-RAY DIFFRACTIONf_plane_restr0.0061445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.35482160.33114624X-RAY DIFFRACTION96
1.9722-1.99540.32212390.30354692X-RAY DIFFRACTION96
1.9954-2.01970.32172420.29664648X-RAY DIFFRACTION96
2.0197-2.04530.27422360.27824755X-RAY DIFFRACTION96
2.0453-2.07220.32912640.26194633X-RAY DIFFRACTION96
2.0722-2.10060.27682760.25494675X-RAY DIFFRACTION96
2.1006-2.13060.27892220.2464728X-RAY DIFFRACTION96
2.1306-2.16240.28512340.23274696X-RAY DIFFRACTION97
2.1624-2.19620.25762240.2244732X-RAY DIFFRACTION96
2.1962-2.23220.28462220.21614665X-RAY DIFFRACTION97
2.2322-2.27070.25282230.21024850X-RAY DIFFRACTION97
2.2707-2.3120.24552380.20144732X-RAY DIFFRACTION97
2.312-2.35650.22312360.20074774X-RAY DIFFRACTION97
2.3565-2.40460.26362800.2074658X-RAY DIFFRACTION97
2.4046-2.45690.26332410.1854770X-RAY DIFFRACTION97
2.4569-2.5140.21462180.18174709X-RAY DIFFRACTION97
2.514-2.57690.22082380.18024856X-RAY DIFFRACTION97
2.5769-2.64660.18672260.1834736X-RAY DIFFRACTION98
2.6466-2.72440.25542480.18614725X-RAY DIFFRACTION98
2.7244-2.81240.22712280.18644824X-RAY DIFFRACTION98
2.8124-2.91290.2312120.19064855X-RAY DIFFRACTION98
2.9129-3.02950.23332980.1824708X-RAY DIFFRACTION98
3.0295-3.16740.24572760.17774739X-RAY DIFFRACTION98
3.1674-3.33440.20452500.17124814X-RAY DIFFRACTION98
3.3344-3.54330.19152740.15764784X-RAY DIFFRACTION98
3.5433-3.81690.16892740.13274864X-RAY DIFFRACTION99
3.8169-4.20090.17022020.13284846X-RAY DIFFRACTION99
4.2009-4.80870.16342680.12474812X-RAY DIFFRACTION99
4.8087-6.05790.18322260.1524876X-RAY DIFFRACTION99
6.0579-70.07210.18512640.16734837X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4223-0.7973-0.24113.33110.48551.4313-0.0793-0.11160.12390.18010.1228-0.1063-0.19720.0359-0.0380.2152-0.00160.0180.1754-0.02270.1986-11.018766.883624.9527
21.7038-0.6892-0.36873.09530.5412.38080.10150.2225-0.1163-0.9028-0.0154-0.0342-00.1411-0.02030.52460.00730.06730.2086-0.03760.2108-4.134530.6873-4.9632
31.6695-0.28840.4942.02240.04411.60430.01840.21780.0645-0.5299-0.11740.5097-0.1457-0.31660.10040.52880.0357-0.14390.3456-0.03990.4686-30.81254.0036-3.7448
42.6655-1.2423-0.31643.83560.29472.1798-0.383-0.5017-0.20441.22150.35770.27830.52070.15450.03370.55930.13680.12910.21460.07860.156-8.557431.73631.7336
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 8 through 251)
2X-RAY DIFFRACTION2(chain 'B' and resid 8 through 251)
3X-RAY DIFFRACTION3(chain 'C' and resid 9 through 252)
4X-RAY DIFFRACTION4(chain 'D' and resid 8 through 251)

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