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- PDB-8yi6: BesA wild-type from Streptomyces cattleyicolor -

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Basic information

Entry
Database: PDB / ID: 8yi6
TitleBesA wild-type from Streptomyces cattleyicolor
ComponentsL-propargylglycine--L-glutamate ligase
KeywordsLIGASE / ATP-grasp protein superfamily / amino acid-ligase / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


L-propargylglycine--L-glutamate ligase activity / L-beta-ethynylserine biosynthetic process / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / antibiotic biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
: / Pre ATP-grasp domain / PGM1 C-terminal domain / PGM1 C-terminal domain / Pre ATP-grasp domain / ATP-grasp fold, PylC-type / ATP-grasp domain
Similarity search - Domain/homology
ADENINE / L-propargylglycine--L-glutamate ligase
Similarity search - Component
Biological speciesStreptantibioticus cattleyicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsFujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H04542 Japan
CitationJournal: To be published
Title: Structure-guided understanding enzymatic mechanism and substrate specificity of ATP-dependent alkyne-containing dipeptide synthetase BesA
Authors: Otsuka, H. / Gouda, A. / Fujishiro, T.
History
DepositionFeb 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-propargylglycine--L-glutamate ligase
B: L-propargylglycine--L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6174
Polymers103,3462
Non-polymers2702
Water00
1
A: L-propargylglycine--L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8082
Polymers51,6731
Non-polymers1351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-propargylglycine--L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8082
Polymers51,6731
Non-polymers1351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.680, 138.680, 144.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein L-propargylglycine--L-glutamate ligase


Mass: 51673.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptantibioticus cattleyicolor (bacteria)
Gene: besA, SCATT_p06910 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: G8XHD8, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 3.37 Å3/Da / Density % sol: 63.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M lithium sulfate, 50% (v/v) PEG 400, 0.1 M sodium acetate, 5 mM ATP, 4 mM L-glutamic acid, 4 mM L-propargylglycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 2.7 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 2, 2022
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7 Å / Relative weight: 1
ReflectionResolution: 3.6→46.45 Å / Num. obs: 16959 / % possible obs: 99.9 % / Redundancy: 8.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.105 / Net I/σ(I): 13.32
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.6-3.71.74513110.7191.8551
3.7-3.81.19611700.7521.2711
3.8-3.90.83910540.880.8921
3.9-40.6069590.9260.6441
4-60.18386210.9920.1951
6-100.04529620.9990.0471
10-46.450.0398820.9980.0421

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XSCALEdata scaling
PHASER2.8.3phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→46.45 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.91 / SU B: 113.35 / SU ML: 0.702 / Cross valid method: THROUGHOUT / ESU R Free: 0.701 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29012 848 5 %RANDOM
Rwork0.23897 ---
obs0.24158 16111 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 170.526 Å2
Baniso -1Baniso -2Baniso -3
1-6.17 Å2-0 Å2-0 Å2
2--6.17 Å20 Å2
3----12.34 Å2
Refinement stepCycle: 1 / Resolution: 3.6→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6990 0 20 0 7010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0127136
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.961.8499680
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.115914
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.759598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.8101142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1590.21090
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025456
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it14.17612.1843662
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it22.36921.894574
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it17.32713.2263474
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined37.065153.7529674
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 61 -
Rwork0.416 1165 -
obs--99.92 %
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)
10.50190.39880.84421.72110.79771.8901-0.03960.0455-0.2607-0.28230.2876-0.2709-0.25770.1382-0.24810.0934-0.057-0.02440.1022-0.23041.0376-0.6612-37.3229-23.2682
20.8841-0.45211.47381.4979-1.13062.6156-0.2342-0.4459-0.1250.07490.193-0.1893-0.4198-0.74840.04120.09640.164-0.00590.30380.11360.80471.8864-33.948224.8701
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 138
2X-RAY DIFFRACTION1A139 - 226
3X-RAY DIFFRACTION1A227 - 277
4X-RAY DIFFRACTION1A278 - 350
5X-RAY DIFFRACTION1A351 - 462
6X-RAY DIFFRACTION2B5 - 138
7X-RAY DIFFRACTION2B139 - 189
8X-RAY DIFFRACTION2B190 - 277
9X-RAY DIFFRACTION2B278 - 350
10X-RAY DIFFRACTION2B351 - 462

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