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- PDB-7twa: Crystal structure of apo BesC from Streptomyces cattleya -

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Basic information

Entry
Database: PDB / ID: 7twa
TitleCrystal structure of apo BesC from Streptomyces cattleya
Components4-chloro-allylglycine synthase
KeywordsBIOSYNTHETIC PROTEIN / Heme-Oxygenase-like Diiron Oxidase
Function / homology
Function and homology information


4-chloro-allylglycine synthase activity / L-propargylglycine biosynthetic process / L-beta-ethynylserine biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous / antibiotic biosynthetic process / metal ion binding
Similarity search - Function
: / Iron-containing redox enzyme / Iron-containing redox enzyme / Pyrroloquinoline-quinone synthase-like / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / 1,3-BUTANEDIOL / 4-chloro-allylglycine synthase
Similarity search - Component
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsNeugebauer, M.E. / McBride, M.J. / Boal, A.K. / Chang, M.C.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Biochemistry / Year: 2022
Title: Substrate-Triggered mu-Peroxodiiron(III) Intermediate in the 4-Chloro-l-Lysine-Fragmenting Heme-Oxygenase-like Diiron Oxidase (HDO) BesC: Substrate Dissociation from, and C4 Targeting by, the Intermediate.
Authors: McBride, M.J. / Nair, M.A. / Sil, D. / Slater, J.W. / Neugebauer, M.E. / Chang, M.C.Y. / Boal, A.K. / Krebs, C. / Bollinger Jr., J.M.
History
DepositionFeb 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-chloro-allylglycine synthase
B: 4-chloro-allylglycine synthase
C: 4-chloro-allylglycine synthase
D: 4-chloro-allylglycine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,67516
Polymers119,0464
Non-polymers62912
Water17,078948
1
A: 4-chloro-allylglycine synthase
D: 4-chloro-allylglycine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8959
Polymers59,5232
Non-polymers3727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-33 kcal/mol
Surface area19630 Å2
MethodPISA
2
B: 4-chloro-allylglycine synthase
hetero molecules

C: 4-chloro-allylglycine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7807
Polymers59,5232
Non-polymers2575
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-x,y-1/2,-z-11
Buried area3090 Å2
ΔGint-27 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.917, 68.977, 126.748
Angle α, β, γ (deg.)90.000, 89.990, 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
4-chloro-allylglycine synthase / L-2-amino-4-chloropent-4-enoate synthase


Mass: 29761.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cattleya (bacteria) / Gene: besC, SCATT_p06890 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: F8JJ25, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous

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Non-polymers , 6 types, 960 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-BU2 / 1,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 948 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.53 % / Description: small hexagonal plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: SeMet crystals were prepared by micro-seeding equal volumes of protein solution (10 mg/mL BesC in 50 mM HEPES pH 7.5 and 1 mM TCEP) and reservoir solution (calcium acetate (0.6 mM), PEG 3350 ...Details: SeMet crystals were prepared by micro-seeding equal volumes of protein solution (10 mg/mL BesC in 50 mM HEPES pH 7.5 and 1 mM TCEP) and reservoir solution (calcium acetate (0.6 mM), PEG 3350 (25% (v/v)) and 1,3 butane-diol (4%))

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Data collection

DiffractionMean temperature: 194 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.95368 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 14, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95368 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 1.7→126.75 Å / Num. obs: 115301 / % possible obs: 99.7 % / Redundancy: 8.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.029 / Rrim(I) all: 0.085 / Net I/σ(I): 14.2 / Num. measured all: 941610 / Scaling rejects: 78
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.736.80.6353634553780.9170.2580.6882.694.6
9.31-126.758.10.06161537550.9990.0220.06532.999.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIX1.13phasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→126.748 Å / Cross valid method: THROUGHOUT / σ(F): 34.43 / Phase error: 36.02 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2471 5740 4.98 %
Rwork0.1988 109463 -
obs0.2355 115276 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.1 Å2 / Biso mean: 20.2981 Å2 / Biso min: 8.25 Å2
Refinement stepCycle: final / Resolution: 1.7→126.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7222 0 39 948 8209
Biso mean--23.97 24.85 -
Num. residues----889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047437
X-RAY DIFFRACTIONf_angle_d0.5410050
X-RAY DIFFRACTIONf_dihedral_angle_d20.1232731
X-RAY DIFFRACTIONf_chiral_restr0.0381070
X-RAY DIFFRACTIONf_plane_restr0.0031318
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7004-1.72970.38822220.35045194541691
1.7297-1.76120.37273130.36565438575194
1.7612-1.7950.36482940.35985437573195
1.795-1.83170.40132840.35995456574095
1.8317-1.87150.4223420.3465438578094
1.8715-1.9150.38742800.33735473575395
1.915-1.96290.36482870.32285466575395
1.9629-2.0160.36323170.30785375569294
2.016-2.07530.29622940.29385486578095
2.0753-2.14230.34972360.29135529576596
2.1423-2.21890.30332430.27755525576896
2.2189-2.30770.27223420.26915409575194
2.3077-2.41270.26542520.24895503575596
2.4127-2.53990.27263360.2385485582194
2.5399-2.6990.28552720.23125496576895
2.699-2.90740.28672720.22325517578995
2.9074-3.19980.28012690.19775537580695
3.1998-3.66260.2422890.18535491578095
3.6626-4.61360.24442720.1575576584895
4.6136-42.26240.22853180.18065632595095

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