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- PDB-8e19: Crystal structure of TnmK1 complexed with TNM H -

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Basic information

Entry
Database: PDB / ID: 8.0E+19
TitleCrystal structure of TnmK1 complexed with TNM H
ComponentsSecreted hydrolase
KeywordsHYDROLASE / biosynthesis
Function / homology: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / SUCCINIC ACID / Chem-U8L / Secreted hydrolase
Function and homology information
Biological speciesStreptomyces sp. CB03234 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 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: J.Am.Chem.Soc. / Year: 2022
Title: Intramolecular C-C Bond Formation Links Anthraquinone and Enediyne Scaffolds in Tiancimycin Biosynthesis.
Authors: Gui, C. / Kalkreuter, E. / Liu, Y.C. / Adhikari, A. / Teijaro, C.N. / Yang, D. / Chang, C. / Shen, B.
History
DepositionAug 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Secreted hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0364
Polymers52,2021
Non-polymers8343
Water6,792377
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.843, 85.843, 129.317
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-908-

HOH

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Components

#1: Protein Secreted hydrolase


Mass: 52201.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. CB03234 (bacteria) / Gene: tnmK1, AMK26_32035 / Production host: Streptomyces lividans (bacteria) / References: UniProt: A0A125SA14
#2: Chemical ChemComp-U8L / (1R,8S,13S)-8-[(4-hydroxy-9,10-dioxo-9,10-dihydroanthracen-1-yl)amino]-12-methoxy-10-methylbicyclo[7.3.1]trideca-9,11-diene-2,6-diyne-13-carbaldehyde


Mass: 477.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H23NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES, pH 7.0, 1.0 M succinic acid, pH 7.0, and 1% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.03→30 Å / Num. obs: 31893 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 27.12 Å2 / CC1/2: 0.998 / Net I/σ(I): 32
Reflection shellResolution: 2.03→2.06 Å / Num. unique obs: 1569 / CC1/2: 0.728

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 8.0E+18 / Resolution: 2.03→29.55 Å / SU ML: 0.2103 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.6859
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2062 1546 4.85 %
Rwork0.1814 30347 -
obs0.1826 31893 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.5 Å2
Refinement stepCycle: LAST / Resolution: 2.03→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3524 0 59 377 3960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00573697
X-RAY DIFFRACTIONf_angle_d0.8355047
X-RAY DIFFRACTIONf_chiral_restr0.0474540
X-RAY DIFFRACTIONf_plane_restr0.0072671
X-RAY DIFFRACTIONf_dihedral_angle_d6.8151549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.10.2951410.24492692X-RAY DIFFRACTION99.26
2.1-2.170.29241200.21952707X-RAY DIFFRACTION100
2.17-2.260.25441270.20792731X-RAY DIFFRACTION100
2.26-2.360.26491260.20382728X-RAY DIFFRACTION100
2.36-2.480.22721520.20092702X-RAY DIFFRACTION100
2.49-2.640.22491310.20072755X-RAY DIFFRACTION100
2.64-2.840.21271410.1842724X-RAY DIFFRACTION100
2.84-3.130.21561490.17852764X-RAY DIFFRACTION100
3.13-3.580.18871430.16632781X-RAY DIFFRACTION100
3.58-4.510.16981610.14792793X-RAY DIFFRACTION99.97
4.51-29.550.18041550.17992970X-RAY DIFFRACTION100

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