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- PDB-9vgl: Ancestral L-tryptophan synthase beta-subunit 1 -

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Basic information

Entry
Database: PDB / ID: 9vgl
TitleAncestral L-tryptophan synthase beta-subunit 1
ComponentsAncestral L-tryptophan synthase beta-subunit 1
KeywordsBIOSYNTHETIC PROTEIN / L-tryptophan synthase
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOhata, M. / Fujita, S. / Uchida, K. / Kobayashi, S. / Chisuga, T. / Nakano, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K17828 Japan
Japan Society for the Promotion of Science (JSPS)23K19283 Japan
CitationJournal: Chemcatchem / Year: 2025
Title: Synthesis of L-Tryptophan Analogs by Ancestral L-Tryptophan Synthase beta-Subunit with High Organic Solvent Tolerance
Authors: Ohata, M. / Fujita, S. / Uchida, K. / Kobayashi, S. / Chisuga, T. / Nakano, S.
History
DepositionJun 14, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ancestral L-tryptophan synthase beta-subunit 1
D: Ancestral L-tryptophan synthase beta-subunit 1
C: Ancestral L-tryptophan synthase beta-subunit 1
B: Ancestral L-tryptophan synthase beta-subunit 1


Theoretical massNumber of molelcules
Total (without water)176,7214
Polymers176,7214
Non-polymers00
Water8,971498
1
A: Ancestral L-tryptophan synthase beta-subunit 1
B: Ancestral L-tryptophan synthase beta-subunit 1


Theoretical massNumber of molelcules
Total (without water)88,3612
Polymers88,3612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-10 kcal/mol
Surface area27650 Å2
MethodPISA
2
D: Ancestral L-tryptophan synthase beta-subunit 1
C: Ancestral L-tryptophan synthase beta-subunit 1


Theoretical massNumber of molelcules
Total (without water)88,3612
Polymers88,3612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-10 kcal/mol
Surface area27610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.529, 91.661, 105.181
Angle α, β, γ (deg.)90.00, 105.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ancestral L-tryptophan synthase beta-subunit 1


Mass: 44180.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG 3350, 200mM ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→47.21 Å / Num. obs: 160314 / % possible obs: 99.3 % / Redundancy: 13.4 % / CC1/2: 1 / Net I/σ(I): 23.8
Reflection shellResolution: 1.7→1.79 Å / Num. unique obs: 160314 / CC1/2: 0.816

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.21 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.522 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 7877 4.9 %RANDOM
Rwork0.19046 ---
obs0.19216 152410 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.036 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.7→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12099 0 0 498 12597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01212323
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611761
X-RAY DIFFRACTIONr_angle_refined_deg1.761.83716659
X-RAY DIFFRACTIONr_angle_other_deg0.6211.76727165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00851553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.584560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.144102197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.21848
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022581
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_it2.212.4036224
X-RAY DIFFRACTIONr_mcbond_other2.2092.4036224
X-RAY DIFFRACTIONr_mcangle_it2.994.3137773
X-RAY DIFFRACTIONr_mcangle_other2.994.3137774
X-RAY DIFFRACTIONr_scbond_it3.0842.7716099
X-RAY DIFFRACTIONr_scbond_other3.0842.7726096
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6334.9398887
X-RAY DIFFRACTIONr_long_range_B_refined5.57424.2513759
X-RAY DIFFRACTIONr_long_range_B_other5.56124.0713662
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 548 -
Rwork0.249 11080 -
obs--97.57 %

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