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- PDB-8g5u: Crystal structure of TnmK2 complexed with TNM B -

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Basic information

Entry
Database: PDB / ID: 8g5u
TitleCrystal structure of TnmK2 complexed with TNM B
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 / Chem-9VG / Secreted hydrolase
Function and homology information
Biological speciesStreptomyces sp. CB03234 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,2878
Polymers214,3134
Non-polymers1,9744
Water36,4442023
1
A: TnmK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0722
Polymers53,5781
Non-polymers4931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TnmK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0722
Polymers53,5781
Non-polymers4931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TnmK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0722
Polymers53,5781
Non-polymers4931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TnmK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0722
Polymers53,5781
Non-polymers4931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.110, 134.110, 355.757
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-1194-

HOH

21A-1196-

HOH

31A-1197-

HOH

41B-1186-

HOH

51B-1189-

HOH

61B-1191-

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: Chemical
ChemComp-9VG / methyl (2E)-3-[(1aS,11S,11aS,14Z,18R)-3,18-dihydroxy-4,9-dioxo-4,9,10,11-tetrahydro-11aH-11,1a-hept[3]ene[1,5]diynonaphtho[2,3-h]oxireno[c]quinolin-11a-yl]but-2-enoate


Mass: 493.464 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H19NO7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2023 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.87 Å3/Da / Density % sol: 57.19 %
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: 1.8→30 Å / Num. obs: 217453 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.997 / Net I/σ(I): 27.9
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 10962 / CC1/2: 0.658

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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: 1.804→29.646 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 11332 5.21 %
Rwork0.189 --
obs0.1904 217453 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.804→29.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14860 0 148 2023 17031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515511
X-RAY DIFFRACTIONf_angle_d0.82321240
X-RAY DIFFRACTIONf_dihedral_angle_d16.3289222
X-RAY DIFFRACTIONf_chiral_restr0.0472307
X-RAY DIFFRACTIONf_plane_restr0.0052820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.804-1.82450.31213230.27415974X-RAY DIFFRACTION86
1.8245-1.8460.31163460.27366540X-RAY DIFFRACTION95
1.846-1.86850.28253450.2586700X-RAY DIFFRACTION96
1.8685-1.89210.26083870.24446747X-RAY DIFFRACTION97
1.8921-1.9170.29124170.24416883X-RAY DIFFRACTION100
1.917-1.94330.26763900.23956932X-RAY DIFFRACTION100
1.9433-1.9710.27543830.23346941X-RAY DIFFRACTION100
1.971-2.00040.24313720.22786918X-RAY DIFFRACTION100
2.0004-2.03170.27853960.22856931X-RAY DIFFRACTION100
2.0317-2.0650.26833840.22296888X-RAY DIFFRACTION100
2.065-2.10060.25263630.21336980X-RAY DIFFRACTION100
2.1006-2.13880.2574080.21516920X-RAY DIFFRACTION100
2.1388-2.17990.24354070.21156881X-RAY DIFFRACTION100
2.1799-2.22440.25654390.20486845X-RAY DIFFRACTION100
2.2244-2.27270.22263860.19626975X-RAY DIFFRACTION100
2.2727-2.32560.23243760.19966886X-RAY DIFFRACTION100
2.3256-2.38370.20363880.19076948X-RAY DIFFRACTION100
2.3837-2.44810.22033930.19196949X-RAY DIFFRACTION100
2.4481-2.52010.20013250.1796980X-RAY DIFFRACTION100
2.5201-2.60140.22313790.18646915X-RAY DIFFRACTION100
2.6014-2.69430.21582940.18147012X-RAY DIFFRACTION100
2.6943-2.80210.18783390.17556976X-RAY DIFFRACTION100
2.8021-2.92960.20353610.17826958X-RAY DIFFRACTION100
2.9296-3.08390.2023920.18296924X-RAY DIFFRACTION100
3.0839-3.27680.21993900.17546916X-RAY DIFFRACTION100
3.2768-3.52950.20373820.17796974X-RAY DIFFRACTION100
3.5295-3.8840.18674450.16656830X-RAY DIFFRACTION100
3.884-4.44440.1963570.14976955X-RAY DIFFRACTION100
4.4444-5.59330.15934220.15536900X-RAY DIFFRACTION100
5.5933-29.6460.18273430.18346943X-RAY DIFFRACTION100

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