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- PDB-4xvh: Crystal structure of a Corynascus thermopiles (Myceliophthora fer... -

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Basic information

Entry
Database: PDB / ID: 4xvh
TitleCrystal structure of a Corynascus thermopiles (Myceliophthora fergusii) carbohydrate esterase family 2 (CE2) enzyme plus carbohydrate binding domain (CBD)
ComponentsCarbohydrate esterase family 2 (CE2)
KeywordsHYDROLASE / fungus / CE2 / carbohydrate esterase / putative acetyl xylan esterase / rossman fold / carbohydrate binding domain / CBD / beta sandwich / jelly roll
Function / homology
Function and homology information


carboxylic ester hydrolase activity
Similarity search - Function
Carbohydrate esterase 2, N-terminal / Carbohydrate esterase 2 N-terminal / CtCE2-like domain / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls ...Carbohydrate esterase 2, N-terminal / Carbohydrate esterase 2 N-terminal / CtCE2-like domain / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Carbohydrate esterase family 2 (CE2)
Similarity search - Component
Biological speciesChaetomium olivicolor (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9449 Å
AuthorsStogios, P.J. / Dong, A. / Xu, X. / Cui, H. / Savchenko, A.
CitationJournal: To Be Published
Title: Crystal structure of a Corynascus thermopiles carbohydrate esterase family 2 (CE2) enzyme plus carbohydrate binding domain (CBD)
Authors: Stogios, P.J. / Dong, A. / Xu, X. / Cui, H. / Savchenko, A.
History
DepositionJan 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 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: Carbohydrate esterase family 2 (CE2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0293
Polymers34,7161
Non-polymers1,3142
Water10,088560
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-7 kcal/mol
Surface area13780 Å2
Unit cell
Length a, b, c (Å)114.730, 134.310, 50.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-552-

HOH

21A-566-

HOH

31A-574-

HOH

41A-589-

HOH

51A-595-

HOH

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Components

#1: Protein Carbohydrate esterase family 2 (CE2)


Mass: 34715.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium olivicolor (fungus) / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0A0J9X278*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEU / 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL / PEG 8000


Mass: 1221.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H112O28 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-tris pH 6.5, 0.2 M sodium acetate, 30% (w/v) PEG 8K. cryoprotectant: paratone-N oil

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Oct 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9449→19.27 Å / Num. obs: 28822 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 24.1
Reflection shellResolution: 1.9449→2.06 Å / Redundancy: 7 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
BALBESphasing
PHENIX(phenix.refine: 1.9_1692)refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WAO

2wao


Resolution: 1.9449→19.122 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1835 1362 5.02 %Random selection
Rwork0.1419 ---
obs0.1441 27145 94.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9449→19.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 29 560 3041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122553
X-RAY DIFFRACTIONf_angle_d1.4243484
X-RAY DIFFRACTIONf_dihedral_angle_d10.791902
X-RAY DIFFRACTIONf_chiral_restr0.061388
X-RAY DIFFRACTIONf_plane_restr0.008454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9499-2.01950.26721170.19172356X-RAY DIFFRACTION87
2.0195-2.10020.21751170.16732401X-RAY DIFFRACTION89
2.1002-2.19570.18781260.15222499X-RAY DIFFRACTION92
2.1957-2.31130.20641340.15382509X-RAY DIFFRACTION92
2.3113-2.45580.21521390.14682517X-RAY DIFFRACTION94
2.4558-2.6450.20931350.15542601X-RAY DIFFRACTION95
2.645-2.91030.21261380.15232644X-RAY DIFFRACTION97
2.9103-3.32950.18041440.14332678X-RAY DIFFRACTION98
3.3295-4.18760.15451650.12012716X-RAY DIFFRACTION98
4.1876-19.12260.15761470.12972862X-RAY DIFFRACTION99
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)
13.6751-0.68560.94871.4175-0.08661.35960.05710.30060.0189-0.29930.0119-0.2134-0.08590.3342-0.06250.198-0.03980.04220.2123-0.01070.1586-13.3615-17.47912.2627
22.1045-2.17930.34083.50531.54113.57140.04510.47560.36850.0037-0.0194-0.4445-0.12320.51190.00730.175-0.04770.03830.2844-0.00260.3046-4.0756-19.24995.2916
34.7145-1.5311-1.46390.93820.78683.1870.08990.6589-0.192-0.2144-0.1209-0.084-0.06060.3790.02630.2318-0.03510.00430.3248-0.03120.1742-12.306-17.01480.3341
41.99260.02660.28892.73150.39331.89010.003-0.05040.15910.02460.02190.0459-0.10290.0284-0.02670.1312-0.0243-0.00320.1187-0.00290.1036-27.4359-16.153111.5804
51.10820.0717-0.22541.95480.14371.83240.00830.01710.0648-0.0694-0.03030.4301-0.0274-0.29560.01620.1474-0.0071-0.03480.1851-0.00780.226-38.4726-18.266411.0744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 24:80)
2X-RAY DIFFRACTION2(chain A and resid 81:103)
3X-RAY DIFFRACTION3(chain A and resid 104:128)
4X-RAY DIFFRACTION4(chain A and resid 129:196)
5X-RAY DIFFRACTION5(chain A and resid 197:352)

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