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- PDB-8e18: Crystal structure of apo TnmK1 -

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Basic information

Entry
Database: PDB / ID: 8.0E+18
TitleCrystal structure of apo TnmK1
ComponentsSecreted hydrolase
KeywordsHYDROLASE / biosynthesis
Function / homology: / 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: 1.14 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)52,6793
Polymers52,2021
Non-polymers4772
Water13,908772
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)86.006, 86.006, 132.392
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-1008-

HOH

21A-1152-

HOH

31A-1264-

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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 772 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.55 %
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: 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: 1.13→30 Å / Num. obs: 172050 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 15.01 Å2 / CC1/2: 0.997 / Net I/σ(I): 56.6
Reflection shellResolution: 1.13→1.15 Å / Num. unique obs: 9157 / CC1/2: 0.723

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UNO

5uno


Resolution: 1.14→29.64 Å / SU ML: 0.0853 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 12.4564
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1526 8587 4.99 %
Rwork0.1326 163463 -
obs0.1336 172050 94.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.58 Å2
Refinement stepCycle: LAST / Resolution: 1.14→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3545 0 30 772 4347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01143769
X-RAY DIFFRACTIONf_angle_d1.27725159
X-RAY DIFFRACTIONf_chiral_restr0.0971554
X-RAY DIFFRACTIONf_plane_restr0.0138691
X-RAY DIFFRACTIONf_dihedral_angle_d11.1305575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.150.3567150.294345X-RAY DIFFRACTION6.01
1.15-1.160.23741650.20172715X-RAY DIFFRACTION48.38
1.16-1.180.1882550.17385126X-RAY DIFFRACTION89.94
1.18-1.190.18652680.15225634X-RAY DIFFRACTION98.65
1.19-1.210.17063200.13955628X-RAY DIFFRACTION99.73
1.21-1.220.15842790.13075722X-RAY DIFFRACTION99.93
1.22-1.240.15363050.11995665X-RAY DIFFRACTION99.97
1.24-1.260.14513060.12045671X-RAY DIFFRACTION100
1.26-1.280.1293020.11825683X-RAY DIFFRACTION100
1.28-1.30.16472780.11795725X-RAY DIFFRACTION100
1.3-1.320.15252950.11435724X-RAY DIFFRACTION100
1.32-1.350.1392950.10895694X-RAY DIFFRACTION99.97
1.35-1.370.1462770.11665738X-RAY DIFFRACTION100
1.37-1.40.14242800.10895692X-RAY DIFFRACTION100
1.4-1.430.14742760.09835753X-RAY DIFFRACTION100
1.43-1.470.12263240.08995691X-RAY DIFFRACTION100
1.47-1.50.11873110.09115709X-RAY DIFFRACTION100
1.5-1.540.10753090.0885711X-RAY DIFFRACTION100
1.54-1.590.11723200.09565706X-RAY DIFFRACTION99.98
1.59-1.640.1263050.09795732X-RAY DIFFRACTION100
1.64-1.70.12522760.10545761X-RAY DIFFRACTION99.98
1.7-1.770.14053040.11985771X-RAY DIFFRACTION100
1.77-1.850.14323130.11915725X-RAY DIFFRACTION100
1.85-1.940.13012900.11975783X-RAY DIFFRACTION100
1.94-2.070.13073140.12295792X-RAY DIFFRACTION99.98
2.07-2.220.14713300.12595767X-RAY DIFFRACTION100
2.23-2.450.14733120.13485826X-RAY DIFFRACTION100
2.45-2.80.16783130.15035858X-RAY DIFFRACTION100
2.8-3.530.17263180.14895920X-RAY DIFFRACTION99.98
3.53-29.640.17213320.15686196X-RAY DIFFRACTION99.97

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