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- PDB-9d1j: The alpha-E7 carboxylesterase from Cochliomyia hominivorax -

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Basic information

Entry
Database: PDB / ID: 9d1j
TitleThe alpha-E7 carboxylesterase from Cochliomyia hominivorax
ComponentsCarboxylic ester hydrolase
KeywordsHYDROLASE / insect esterase / carboxylesterase
Function / homologyHydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold / Carboxylic ester hydrolase
Function and homology information
Biological speciesCochliomyia hominivorax (primary screw-worm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsFrkic, R.L. / Fraser, N. / Mabbitt, P.D. / Jackson, C.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100012 Australia
Australian Research Council (ARC)CE200100029 Australia
CitationJournal: To Be Published
Title: The alpha-E7 carboxylesterase from Cochliomyia hominivorax
Authors: Frkic, R.L. / Fraser, N. / Correy, G. / Mabbitt, P.D. / Jackson, C.J.
History
DepositionAug 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxylic ester hydrolase


Theoretical massNumber of molelcules
Total (without water)65,4701
Polymers65,4701
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.572, 92.559, 106.076
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carboxylic ester hydrolase


Mass: 65469.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cochliomyia hominivorax (primary screw-worm)
Gene: ChaE7 / Production host: Escherichia coli (E. coli)
References: UniProt: C5IWW7, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20-25% PEG 3350, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.03→45.3 Å / Num. obs: 38695 / % possible obs: 100 % / Redundancy: 10.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.048 / Rrim(I) all: 0.166 / Χ2: 1.03 / Net I/σ(I): 8.7 / Num. measured all: 422995
Reflection shellResolution: 2.03→2.08 Å / % possible obs: 100 % / Redundancy: 10.1 % / Rmerge(I) obs: 2.952 / Num. measured all: 28427 / Num. unique obs: 2806 / CC1/2: 0.545 / Rpim(I) all: 0.955 / Rrim(I) all: 3.106 / Χ2: 1.09 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→45.3 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2404 1885 4.89 %
Rwork0.1984 --
obs0.2004 38587 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4597 0 0 95 4692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.802
X-RAY DIFFRACTIONf_dihedral_angle_d6.687647
X-RAY DIFFRACTIONf_chiral_restr0.051680
X-RAY DIFFRACTIONf_plane_restr0.006820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.41931410.3772757X-RAY DIFFRACTION100
2.08-2.150.3711440.32442792X-RAY DIFFRACTION100
2.15-2.220.33351490.28682801X-RAY DIFFRACTION100
2.22-2.290.32971460.26992767X-RAY DIFFRACTION100
2.29-2.390.27921490.24892792X-RAY DIFFRACTION100
2.39-2.50.29511390.24112782X-RAY DIFFRACTION100
2.5-2.630.31221460.22972790X-RAY DIFFRACTION100
2.63-2.790.25151470.22432801X-RAY DIFFRACTION100
2.79-3.010.25111410.22532829X-RAY DIFFRACTION100
3.01-3.310.23851440.21212842X-RAY DIFFRACTION100
3.31-3.790.24011540.19072838X-RAY DIFFRACTION100
3.79-4.770.21521470.15832869X-RAY DIFFRACTION100
4.77-45.30.17581380.15513042X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.56830.41150.30862.5980.55211.1354-0.1239-0.06310.0340.15490.0444-0.2046-0.10540.0390.10660.53940.01410.16510.4028-0.0450.4685-29.33197.580830.5105
21.6174-0.5036-0.06162.62210.26371.1157-0.0122-0.1061-0.03760.1516-0.0463-0.31610.00290.08920.05880.3808-0.04730.05820.34180.01570.3535-19.7802-11.490624.1969
31.7097-0.5377-0.94732.01581.09011.52340.15660.15920.1352-0.55830.0501-0.3625-0.24090.1302-0.19050.74860.00350.1410.45530.01370.4407-16.69960.31053.7066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 58 )
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 341 )
3X-RAY DIFFRACTION3chain 'A' and (resid 342 through 570 )

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