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- PDB-8es6: Crystal structure of an unusual amidase ClbL from colibactin gene... -

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Basic information

Entry
Database: PDB / ID: 8es6
TitleCrystal structure of an unusual amidase ClbL from colibactin gene cluster
ComponentsColibactin biosynthesis amidase ClbL
KeywordsBIOSYNTHETIC PROTEIN / Amidase / Colibactin / Cancer
Function / homology: / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / endomembrane system / Colibactin biosynthesis amidase ClbL
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTripathi, P. / Bruner, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin.
Authors: Tripathi, P. / Mousa, J.J. / Guntaka, N.S. / Bruner, S.D.
History
DepositionOct 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Colibactin biosynthesis amidase ClbL
B: Colibactin biosynthesis amidase ClbL


Theoretical massNumber of molelcules
Total (without water)107,5692
Polymers107,5692
Non-polymers00
Water4,648258
1
A: Colibactin biosynthesis amidase ClbL


Theoretical massNumber of molelcules
Total (without water)53,7851
Polymers53,7851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Colibactin biosynthesis amidase ClbL


Theoretical massNumber of molelcules
Total (without water)53,7851
Polymers53,7851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.924, 56.372, 145.019
Angle α, β, γ (deg.)90.000, 91.840, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Colibactin biosynthesis amidase ClbL / Putative amidase


Mass: 53784.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: clbL, C1Q91_005015, D3C88_26935, E3O05_09855, E4T84_20070, ELT23_23620, ELT33_24240, ELT38_03815, ELY31_20800, EWK56_23785, FPI65_12350, H0O51_25470, HMW38_10405, IFB95_001929
Production host: Escherichia coli (E. coli) / References: UniProt: Q0P7K2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, pH 8.5, 30% PEG3500

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.9→49.55 Å / Num. obs: 66681 / % possible obs: 99.88 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1258 / Net I/σ(I): 10.74
Reflection shellResolution: 1.9→1.96 Å / Num. unique obs: 6614 / CC1/2: 0.73

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5H6S

5h6s


Resolution: 1.9→49.55 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2491 3213 4.82 %
Rwork0.2057 63468 -
obs0.2079 66681 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.11 Å2 / Biso mean: 34.6048 Å2 / Biso min: 12.84 Å2
Refinement stepCycle: final / Resolution: 1.9→49.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6695 0 0 258 6953
Biso mean---31.04 -
Num. residues----858
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.920.40671170.3519263895
1.92-1.950.31811040.30082791100
1.95-1.990.32711480.29012716100
1.99-2.020.30811340.27142777100
2.02-2.060.29941370.26272732100
2.06-2.10.3611280.25462773100
2.1-2.140.31671230.24382712100
2.14-2.190.31621160.24342821100
2.19-2.240.34591390.24612715100
2.24-2.290.31731360.22862769100
2.29-2.360.27281330.23322788100
2.36-2.420.30821110.22192759100
2.42-2.50.28071430.22462737100
2.5-2.590.29831210.23092807100
2.59-2.70.28571650.22892730100
2.7-2.820.2921550.23212754100
2.82-2.970.2791670.2212739100
2.97-3.150.27451550.2062728100
3.15-3.40.23111540.20072750100
3.4-3.740.20521800.17632766100
3.74-4.280.17911170.15992820100
4.28-5.390.17461700.14762784100

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