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- PDB-4psc: Structure of cutinase from Trichoderma reesei in its native form. -

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Basic information

Entry
Database: PDB / ID: 4psc
TitleStructure of cutinase from Trichoderma reesei in its native form.
ComponentsCarbohydrate esterase family 5
KeywordsHYDROLASE / alpha/beta hydrolase fold / cutinase
Function / homology
Function and homology information


cutinase / cutinase activity / carbohydrate catabolic process / extracellular region
Similarity search - Function
Cutinase, monofunctional / Cutinase, aspartate and histidine active sites / Cutinase, serine active site / Cutinase, serine active site. / Cutinase, aspartate and histidine active sites. / Cutinase / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold ...Cutinase, monofunctional / Cutinase, aspartate and histidine active sites / Cutinase, serine active site / Cutinase, serine active site. / Cutinase, aspartate and histidine active sites. / Cutinase / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesTrichoderma reesei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsRoussel, A. / Amara, S. / Nyyssola, A. / Mateos-Diaz, E. / Blangy, S. / Kontkanen, H. / Westerholm-Parvinen, A. / Carriere, F. / Cambillau, C.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: A Cutinase from Trichoderma reesei with a Lid-Covered Active Site and Kinetic Properties of True Lipases.
Authors: Roussel, A. / Amara, S. / Nyyssola, A. / Mateos-Diaz, E. / Blangy, S. / Kontkanen, H. / Westerholm-Parvinen, A. / Carriere, F. / Cambillau, C.
History
DepositionMar 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Structure summary
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Dec 17, 2014Group: Database references
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbohydrate esterase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8622
Polymers26,7701
Non-polymers921
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.159, 48.002, 141.579
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 Carbohydrate esterase family 5


Mass: 26770.236 Da / Num. of mol.: 1 / Fragment: mature form
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma reesei (fungus) / Strain: QM6a / Gene: TRIREDRAFT_60489 / Production host: Trichoderma reesei (fungus) / References: UniProt: G0RH85
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
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: 1.85 Å3/Da / Density % sol: 33.54 %
Crystal growTemperature: 293 K / pH: 5.5
Details: mixing 300 nl enzyme at 10 mg/ml with 100 nl of PEG3350 (25%), Sodium Chloride (0.2 M), BIS-TRIS (0.1 M), pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2011
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR AND A NEW TORODIAL FOCUSING MIRROR.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.15→79.32 Å / Num. obs: 81001 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.3
Reflection shellRedundancy: 2.5 %

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CEX

1cex


Resolution: 1.15→79.32 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.983 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.167 3556 4.9 %RANDOM
Rwork0.146 ---
obs0.147 68635 97.9 %-
all-76957 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å2-0 Å2
2--0.16 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.15→79.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1603 0 6 289 1898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021690
X-RAY DIFFRACTIONr_bond_other_d0.0050.021641
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.9652324
X-RAY DIFFRACTIONr_angle_other_deg1.1213.0033737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6685234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77326.2564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77315254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.817152
X-RAY DIFFRACTIONr_chiral_restr0.1360.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211968
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02354
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr6.61633331
X-RAY DIFFRACTIONr_sphericity_free22.351566
X-RAY DIFFRACTIONr_sphericity_bonded6.97153509
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 234 -
Rwork0.19 4171 -
obs--85.07 %

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