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- PDB-8g5t: Crystal structure of apo TnmK2 -

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Basic information

Entry
Database: PDB / ID: 8g5t
TitleCrystal structure of apo TnmK2
ComponentsTnmK2
KeywordsBIOSYNTHETIC PROTEIN / Biosynthesis / Natural Product / Tiancimycin / Enediyne
Function / homologyPeptidase S33 tripeptidyl aminopeptidase-like, C-terminal / TAP-like protein / : / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Secreted hydrolase
Function and homology information
Biological speciesStreptomyces sp. CB03234 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.846 Å
AuthorsLiu, Y.-C. / Gui, C. / Shen, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134954 United States
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Cofactorless oxygenases guide anthraquinone-fused enediyne biosynthesis.
Authors: Gui, C. / Kalkreuter, E. / Liu, Y.C. / Li, G. / Steele, A.D. / Yang, D. / Chang, C. / Shen, B.
History
DepositionFeb 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TnmK2
B: TnmK2
C: TnmK2
D: TnmK2


Theoretical massNumber of molelcules
Total (without water)214,3134
Polymers214,3134
Non-polymers00
Water25,8881437
1
A: TnmK2


Theoretical massNumber of molelcules
Total (without water)53,5781
Polymers53,5781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TnmK2


Theoretical massNumber of molelcules
Total (without water)53,5781
Polymers53,5781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TnmK2


Theoretical massNumber of molelcules
Total (without water)53,5781
Polymers53,5781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TnmK2


Theoretical massNumber of molelcules
Total (without water)53,5781
Polymers53,5781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.123, 134.123, 356.174
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-949-

HOH

21A-955-

HOH

31A-972-

HOH

41A-973-

HOH

51A-974-

HOH

61B-956-

HOH

71B-958-

HOH

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Components

#1: Protein
TnmK2


Mass: 53578.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. CB03234 (bacteria) / Gene: tnmK2, AMK26_32040 / Production host: Streptomyces lividans (bacteria) / References: UniProt: A0A125SA15
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1437 / 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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M calcium acetate, 0.1 M imidazole/HCl, pH 8.0, 20% w/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.846→30 Å / Num. obs: 197921 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.997 / Net I/σ(I): 30.2
Reflection shellResolution: 1.85→1.88 Å / Num. unique obs: 10218 / CC1/2: 0.714

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Processing

Software
NameVersionClassification
PHENIX(dev_2689: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.846→29.681 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 10149 5.13 %
Rwork0.2259 --
obs0.2272 197921 96.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.846→29.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14860 0 0 1437 16297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515248
X-RAY DIFFRACTIONf_angle_d0.84420820
X-RAY DIFFRACTIONf_dihedral_angle_d13.2589056
X-RAY DIFFRACTIONf_chiral_restr0.0482272
X-RAY DIFFRACTIONf_plane_restr0.0062784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8463-1.86730.33172880.29474439X-RAY DIFFRACTION69
1.8673-1.88930.31922470.27614913X-RAY DIFFRACTION75
1.8893-1.91230.31912980.29295184X-RAY DIFFRACTION81
1.9123-1.93650.31243140.2875475X-RAY DIFFRACTION85
1.9365-1.9620.31133100.27735850X-RAY DIFFRACTION90
1.962-1.98880.31053660.26416258X-RAY DIFFRACTION97
1.9888-2.01720.28663550.27256374X-RAY DIFFRACTION99
2.0172-2.04730.33462680.27236624X-RAY DIFFRACTION100
2.0473-2.07930.29363490.24916485X-RAY DIFFRACTION100
2.0793-2.11340.28613160.2476538X-RAY DIFFRACTION100
2.1134-2.14980.25663860.25376475X-RAY DIFFRACTION100
2.1498-2.18890.27373930.25526398X-RAY DIFFRACTION100
2.1889-2.2310.28323630.25496480X-RAY DIFFRACTION100
2.231-2.27650.26293160.23356578X-RAY DIFFRACTION100
2.2765-2.3260.27323330.24016439X-RAY DIFFRACTION100
2.326-2.38010.2553200.24116517X-RAY DIFFRACTION100
2.3801-2.43960.28454140.24626470X-RAY DIFFRACTION100
2.4396-2.50550.2733780.23476374X-RAY DIFFRACTION100
2.5055-2.57920.24763870.22616502X-RAY DIFFRACTION100
2.5792-2.66240.26953540.23386488X-RAY DIFFRACTION100
2.6624-2.75750.27773780.23176429X-RAY DIFFRACTION100
2.7575-2.86780.25963960.22516436X-RAY DIFFRACTION100
2.8678-2.99820.25463380.22816536X-RAY DIFFRACTION100
2.9982-3.15610.27162990.2236514X-RAY DIFFRACTION100
3.1561-3.35360.23772630.21116557X-RAY DIFFRACTION100
3.3536-3.61210.24693660.2166475X-RAY DIFFRACTION100
3.6121-3.97490.20043300.20016500X-RAY DIFFRACTION100
3.9749-4.54830.20653340.18636518X-RAY DIFFRACTION100
4.5483-5.72360.20073970.18736433X-RAY DIFFRACTION100
5.7236-29.6810.21442930.19736513X-RAY DIFFRACTION99

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