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- PDB-8tru: Crystal structure of a CE15 from Fibrobacter succinogenes subsp. ... -

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Basic information

Entry
Database: PDB / ID: 8tru
TitleCrystal structure of a CE15 from Fibrobacter succinogenes subsp. succinogenes S85
ComponentsGlucuronyl esterase
KeywordsHYDROLASE / carbohydrate / esterase / glucuronyl esterase
Function / homologyGlucuronyl esterase, fungi / Alpha/Beta hydrolase fold / Putative lipoprotein
Function and homology information
Biological speciesFibrobacter succinogenes subsp. succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGruninger, R.J. / Jones, D.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Other government Canada
CitationJournal: Protein J. / Year: 2024
Title: Structural, Biochemical, and Phylogenetic Analysis of Bacterial and Fungal Carbohydrate Esterase Family 15 Glucuronoyl Esterases in the Rumen.
Authors: Gruninger, R.J. / Kevorkova, M. / Low, K.E. / Jones, D.R. / Worrall, L. / McAllister, T.A. / Abbott, D.W.
History
DepositionAug 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucuronyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7783
Polymers44,6471
Non-polymers1312
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.280, 57.280, 222.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-904-

HOH

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Components

#1: Protein Glucuronyl esterase


Mass: 44647.453 Da / Num. of mol.: 1 / Fragment: residues 153-536
Source method: isolated from a genetically manipulated source
Details: C-terminal His-tagged construct
Source: (gene. exp.) Fibrobacter succinogenes subsp. succinogenes (bacteria)
Strain: ATCC 19169 / S85 / Gene: FSU_2898 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C9RKY6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.21 Å3/Da / Density % sol: 39.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20% PEG6000, 100 mM sodium acetate, pH 5.0, 10 mM zinc chloride
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.0334 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2019
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0334 Å / Relative weight: 1
ReflectionResolution: 1.9→19.94 Å / Num. obs: 30281 / % possible obs: 99.98 % / Redundancy: 12.5 % / Biso Wilson estimate: 20.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.051 / Rrim(I) all: 0.179 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.9-1.9712.91.1342.229690.8370.3261.181
1.97-2.05130.882.929590.9020.2530.916
2.05-2.1412.60.6973.729480.9220.20.916
2.14-2.2512.70.5424.929810.9570.1580.565
2.25-2.3912.70.4516.529860.9730.1290.37
2.39-2.5812.70.3558.219790.9820.1040.37
2.58-2.8412.70.26510.930300.990.0770.277
2.84-3.2512.50.17815.230390.9950.0520.277
3.25-4.08120.10422.431070.9980.0310.109
4.08-19.9411.20.07226.332830.9990.0220.076

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.937 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2562 1512 4.99 %
Rwork0.2072 --
obs0.2096 30274 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.14 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2851 0 2 245 3098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062919
X-RAY DIFFRACTIONf_angle_d0.7663942
X-RAY DIFFRACTIONf_dihedral_angle_d4.4382378
X-RAY DIFFRACTIONf_chiral_restr0.049413
X-RAY DIFFRACTIONf_plane_restr0.005520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96130.36611320.34412537X-RAY DIFFRACTION100
1.9613-2.03130.36121360.30692574X-RAY DIFFRACTION100
2.0313-2.11260.31151340.27612553X-RAY DIFFRACTION100
2.1126-2.20860.31791360.2492580X-RAY DIFFRACTION100
2.2086-2.32490.3231340.23592546X-RAY DIFFRACTION100
2.3249-2.47030.28891360.22692593X-RAY DIFFRACTION100
2.4703-2.66060.28291360.23372588X-RAY DIFFRACTION100
2.6606-2.92760.2591370.22842614X-RAY DIFFRACTION100
2.9276-3.34950.28441390.20772638X-RAY DIFFRACTION100
3.3495-4.21350.21621410.16532684X-RAY DIFFRACTION100
4.2135-19.9370.18261510.15882855X-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)
11.85470.16220.22141.33660.05340.3484-0.11170.090.2724-0.05930.07220.0169-0.16330.01760.04540.2754-0.01130.02560.2643-0.00860.4407-29.988524.663219.7542
21.33610.44610.35170.4293-0.11490.5007-0.23170.3186-0.0053-0.14430.1938-0.18630.02770.03570.01210.2513-0.06860.0920.3083-0.09220.4702-14.172718.165316.0936
30.16750.2524-0.07170.4476-0.15790.058-0.31960.402-0.2868-0.11370.1586-0.21990.1617-0.04830.04820.383-0.14580.19950.502-0.20920.6983-9.54353.61067.8839
40.97620.40910.0761.0260.04450.3027-0.12290.1435-0.1967-0.10250.1283-0.10280.00270.05860.00580.2434-0.0260.07060.3044-0.06950.4295-23.68096.544518.6242
50.8331-0.3393-0.19570.16650.11160.0986-0.19040.2749-0.3712-0.28060.18870.07010.0839-0.1008-0.00460.4174-0.12330.09840.4626-0.16880.4063-30.45030.82932.1076
61.0548-0.31490.2882.41470.2350.4563-0.22470.24740.1280.14230.1710.4339-0.0006-0.13280.08160.2288-0.02060.04330.3329-0.00140.4352-42.878611.031617.1893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 155 through 191 )
2X-RAY DIFFRACTION2chain 'A' and (resid 192 through 238 )
3X-RAY DIFFRACTION3chain 'A' and (resid 239 through 274 )
4X-RAY DIFFRACTION4chain 'A' and (resid 275 through 486 )
5X-RAY DIFFRACTION5chain 'A' and (resid 487 through 514 )
6X-RAY DIFFRACTION6chain 'A' and (resid 515 through 538 )

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