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- PDB-8jsu: The crystal structure of TvaE in complex with TvaLP -

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Basic information

Entry
Database: PDB / ID: 8jsu
TitleThe crystal structure of TvaE in complex with TvaLP
Components
  • TvaE
  • TvaLP
KeywordsLYASE / TvaE / Cyclase / Michael addition
Function / homologyBROMIDE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesStreptomyces sp. NRRL S-87 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsLi, M. / Pan, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21822705 China
CitationJournal: Nat.Chem. / Year: 2025
Title: Pseudokinases Can Catalyze Peptide Cyclization through Thioether Crosslinking
Authors: Li, M. / Pan, L.F.
History
DepositionJun 20, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 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: TvaLP
B: TvaE
C: TvaLP
D: TvaE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,01315
Polymers75,2034
Non-polymers81011
Water12,340685
1
A: TvaLP
B: TvaE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1109
Polymers37,6012
Non-polymers5097
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-25 kcal/mol
Surface area15920 Å2
MethodPISA
2
C: TvaLP
D: TvaE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9036
Polymers37,6012
Non-polymers3014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-17 kcal/mol
Surface area16730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.224, 52.499, 73.673
Angle α, β, γ (deg.)94.72, 90.55, 112.55
Int Tables number1
Space group name H-MP1

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Components

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Protein/peptide / Protein , 2 types, 4 molecules ACBD

#1: Protein/peptide TvaLP


Mass: 4258.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. NRRL S-87 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein TvaE


Mass: 33342.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. NRRL S-87 (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 696 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 685 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Amino acids(0.02 M DL-Glutamic acid monohydrate, 0.02 M DL-Alanine, 0.02 M Glycine, 0.02 M DL-Lysine monohydrochloride, 0.02 M DL-Serine), 0.1 M Buffer System 2 (0.05 M Sodium HEPES, 0. ...Details: 0.1 M Amino acids(0.02 M DL-Glutamic acid monohydrate, 0.02 M DL-Alanine, 0.02 M Glycine, 0.02 M DL-Lysine monohydrochloride, 0.02 M DL-Serine), 0.1 M Buffer System 2 (0.05 M Sodium HEPES, 0.05M MOPS(acid)) pH=7.5, 50% v/v Precipitant Mix4 (12.5% v/v MPD, 12.5% v/v PEG 1000, 12.5% v/v PEG3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.44→42.17 Å / Num. obs: 105078 / % possible obs: 92.3 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.2
Reflection shellResolution: 1.44→1.45 Å / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 10353 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIX(1.20.1_4487)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→40.14 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1969 5265 5.01 %
Rwork0.1727 --
obs0.1739 105078 92.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→40.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5199 0 38 685 5922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075601
X-RAY DIFFRACTIONf_angle_d0.9667681
X-RAY DIFFRACTIONf_dihedral_angle_d6.614874
X-RAY DIFFRACTIONf_chiral_restr0.075877
X-RAY DIFFRACTIONf_plane_restr0.0161039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.450.30641730.27543318X-RAY DIFFRACTION92
1.45-1.470.28111870.25673323X-RAY DIFFRACTION92
1.47-1.490.25281720.243282X-RAY DIFFRACTION92
1.49-1.510.26071930.2313354X-RAY DIFFRACTION92
1.51-1.530.21931830.21713214X-RAY DIFFRACTION92
1.53-1.550.22771570.21713358X-RAY DIFFRACTION91
1.55-1.570.23341750.20643368X-RAY DIFFRACTION93
1.57-1.590.25741720.19963320X-RAY DIFFRACTION92
1.59-1.620.22141880.19843288X-RAY DIFFRACTION92
1.62-1.640.20981700.19213342X-RAY DIFFRACTION93
1.64-1.670.24551730.17993400X-RAY DIFFRACTION93
1.67-1.70.21061390.18853416X-RAY DIFFRACTION93
1.7-1.740.23481430.18893389X-RAY DIFFRACTION93
1.74-1.770.21491590.18723324X-RAY DIFFRACTION93
1.77-1.810.20471950.18273381X-RAY DIFFRACTION92
1.81-1.850.20162020.18353245X-RAY DIFFRACTION93
1.85-1.90.20881780.17673370X-RAY DIFFRACTION93
1.9-1.950.22241830.17353342X-RAY DIFFRACTION92
1.95-2.010.18561810.16693300X-RAY DIFFRACTION93
2.01-2.070.20151560.17153385X-RAY DIFFRACTION93
2.07-2.140.20311860.16473345X-RAY DIFFRACTION93
2.14-2.230.16651720.16043313X-RAY DIFFRACTION92
2.23-2.330.1661440.16023326X-RAY DIFFRACTION92
2.33-2.460.17421670.16493357X-RAY DIFFRACTION92
2.46-2.610.20921880.16683297X-RAY DIFFRACTION92
2.61-2.810.17281850.16393322X-RAY DIFFRACTION92
2.81-3.090.19821750.16743269X-RAY DIFFRACTION91
3.09-3.540.18731980.15453303X-RAY DIFFRACTION92
3.54-4.460.16091670.13583308X-RAY DIFFRACTION92
4.46-40.140.17182040.16213254X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: -3.4384 Å / Origin y: -0.6568 Å / Origin z: -15.6466 Å
111213212223313233
T0.0496 Å20.0103 Å20.0164 Å2-0.0778 Å20.0124 Å2--0.0766 Å2
L0.4751 °20.2184 °20.294 °2-0.3557 °20.3614 °2--0.6881 °2
S-0.0169 Å °0.013 Å °-0.0019 Å °-0.0203 Å °0.0067 Å °-0.0079 Å °-0.0247 Å °-0.0089 Å °0.0109 Å °
Refinement TLS groupSelection details: all

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