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- PDB-5ugz: Crystal structure of ClbQ from the colibactin NRPS/PKS pathway -

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Basic information

Entry
Database: PDB / ID: 5ugz
TitleCrystal structure of ClbQ from the colibactin NRPS/PKS pathway
ComponentsPutative thioesterase
KeywordsHYDROLASE / Type-II thioesterase / Colibactin
Function / homologyOxidoreductases; Acting on the CH-OH group of donors / Thioesterase type II, NRPS/PKS/S-FAS / Thioesterase / Thioesterase domain / lipid biosynthetic process / Alpha/Beta hydrolase fold / oxidoreductase activity / BETA-MERCAPTOETHANOL / Thioesterase
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.983 Å
AuthorsGuntaka, N.S. / Bruner, S.D.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Structure and Functional Analysis of ClbQ, an Unusual Intermediate-Releasing Thioesterase from the Colibactin Biosynthetic Pathway.
Authors: Guntaka, N.S. / Healy, A.R. / Crawford, J.M. / Herzon, S.B. / Bruner, S.D.
History
DepositionJan 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative thioesterase
B: Putative thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2324
Polymers59,0762
Non-polymers1562
Water4,053225
1
A: Putative thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6162
Polymers29,5381
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6162
Polymers29,5381
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.971, 94.994, 68.444
Angle α, β, γ (deg.)90.00, 109.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative thioesterase / Thioesterase


Mass: 29537.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clbQ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0P7K7
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, Lithium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9767 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9767 Å / Relative weight: 1
ReflectionResolution: 1.98→38.78 Å / Num. obs: 36972 / % possible obs: 98.3 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.416 / Net I/σ(I): 19.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FLB

3flb


Resolution: 1.983→38.775 Å / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 29.48
RfactorNum. reflection% reflection
Rfree0.2076 1932 5.23 %
Rwork0.1512 --
obs0.1548 36949 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.983→38.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 8 225 4067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073950
X-RAY DIFFRACTIONf_angle_d0.9025358
X-RAY DIFFRACTIONf_dihedral_angle_d13.1952314
X-RAY DIFFRACTIONf_chiral_restr0.05588
X-RAY DIFFRACTIONf_plane_restr0.005686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9848-2.03440.28671470.20462417X-RAY DIFFRACTION91
2.0344-2.08930.25661530.18642449X-RAY DIFFRACTION92
2.0893-2.15080.22411280.19392507X-RAY DIFFRACTION93
2.1508-2.22010.24511240.18072499X-RAY DIFFRACTION94
2.2201-2.29940.22141250.1762492X-RAY DIFFRACTION94
2.2994-2.39140.23971490.16722498X-RAY DIFFRACTION93
2.3914-2.50010.23451520.16762491X-RAY DIFFRACTION93
2.5001-2.63170.26171220.17032523X-RAY DIFFRACTION94
2.6317-2.79630.20811390.16572484X-RAY DIFFRACTION94
2.7963-3.01170.21961410.16012536X-RAY DIFFRACTION94
3.0117-3.31390.19341090.1512502X-RAY DIFFRACTION95
3.3139-3.79140.19311390.13432558X-RAY DIFFRACTION94
3.7914-4.76920.16561390.1122503X-RAY DIFFRACTION93
4.7692-22.41790.17341330.13432555X-RAY DIFFRACTION93

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