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- PDB-4pse: Trichoderma reesei cutinase in complex with a C11Y4 phosphonate i... -

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Basic information

Entry
Database: PDB / ID: 4pse
TitleTrichoderma reesei cutinase in complex with a C11Y4 phosphonate inhibitor
ComponentsCarbohydrate esterase family 5
Keywordshydrolase/hydrolase inhibitor / alpha/beta hydrolase / hydrolase / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


cutinase activity / cutinase / 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
Similarity search - Domain/homology
UNDECYL-PHOSPHINIC ACID BUTYL ESTER / Cutinase
Similarity search - Component
Biological speciesTrichoderma reesei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbohydrate esterase family 5
B: Carbohydrate esterase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6786
Polymers53,5402
Non-polymers1,1384
Water3,495194
1
A: Carbohydrate esterase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6314
Polymers26,7701
Non-polymers8613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbohydrate esterase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0472
Polymers26,7701
Non-polymers2761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.043, 37.544, 133.009
Angle α, β, γ (deg.)90.00, 97.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbohydrate esterase family 5


Mass: 26770.236 Da / Num. of mol.: 2 / Fragment: mature form, complexed
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-C11 / UNDECYL-PHOSPHINIC ACID BUTYL ESTER


Mass: 276.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H33O2P
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: mixing 300 nl enzyme at 10 mg/ml and 30 mM betaOG with 100 nl of PEG3350 (17%), BIS-TRIS (0.1 M), pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2014
RadiationMonochromator: bent cylindrical mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. all: 51222 / Num. obs: 51222 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.8
Reflection shellResolution: 1.71→1.78 Å / Redundancy: 4 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.15 / Num. unique all: 5652 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4PSC

4psc


Resolution: 1.71→47.66 Å / Cor.coef. Fo:Fc: 0.9061 / Cor.coef. Fo:Fc free: 0.9 / SU R Cruickshank DPI: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 2627 5.13 %RANDOM
Rwork0.2199 ---
obs0.2207 51220 97.39 %-
all-51220 --
Displacement parametersBiso mean: 48.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.7128 Å20 Å20.0736 Å2
2---13.3168 Å20 Å2
3---14.0297 Å2
Refine analyzeLuzzati coordinate error obs: 0.264 Å
Refinement stepCycle: LAST / Resolution: 1.71→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 0 75 194 3451
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093338HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.154549HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d01097SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes078HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0484HARMONIC5
X-RAY DIFFRACTIONt_it03338HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion19.85
X-RAY DIFFRACTIONt_chiral_improper_torsion0451SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact04239SEMIHARMONIC4
LS refinement shellResolution: 1.71→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3196 198 5.32 %
Rwork0.3127 3523 -
all0.313 3721 -
obs--97.39 %
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)
10.03670.0194-0.01490.00560.01130.02880.00030.0012-0.0012-0.00120.0005-0.00080.00070.0007-0.0008-0.0123-0.01530.00220.00910.00250.000323.10276.215940.2502
20.0309-0.05680.06710.0048-0.26420.0169-0.0001-0.0018-0.00140.00130.0072-0.00140.00220.0027-0.00710.0106-0.00790.0073-0.00760.04190.001616.288618.028639.8181
30.0407-0.8729-0.15450.0594-0.3831-0.0407-0.00450.00370.0161-0.00490.00280.0136-0.0084-0.00490.0017-0.00770.0403-0.0447-0.01730.04690.0254-3.977113.13548.9891
40.6432-0.74350.10030.31520.00610.1289-0.0065-0.02380.0286-0.0355-0.00960.0432-0.0279-0.06140.0161-0.0718-0.0223-0.0176-0.02490.03170.0831-3.91672.279355.9669
5-0.1127-0.02230.56991.2454-0.16210.2383-0.00440.02630.01720.00090.00460.0006-0.0210.0084-0.0003-0.0203-0.0478-0.0224-0.0610.01770.064111.16317.25654.4065
60.17810.1222-0.0910.73140.2227-0.0244-0.0056-0.02680.03180.00270.00560.0051-0.0077-0.02390-0.0169-0.0139-0.0176-0.05520.00990.0696.00080.876162.6405
7-0.0172-0.69090.50290.534-0.41730.2538-0.00780.0405-0.01790.0060.0169-0.020.0201-0.0104-0.009-0.0158-0.0186-0.0188-0.09310.00610.103510.7746-6.539657.8107
80.1275-0.20470.39090.2111-0.06550.6524-0.00530.0243-0.0187-0.0090.0050.01290.01910.00890.0002-0.0115-0.0785-0.00330.02970.008-0.02314.2995-4.107942.2856
90.07890.40910.05450.0334-0.13220.0128-0.0037-0.0037-0.001-0.00150.00320.00840.0038-0.00120.0005-0.0373-0.0554-0.00160.00640.02680.0315-4.6826-10.48258.625
100.0206-0.0083-0.01640-0.021-0.0045-0.0001-0.00010.0007-0.0005-0.00030.0004-0.0014-0.00050.0004-0.00090.00140.00110.006-0.00050.001-11.01647.206524.0143
110.0170.01610.03490.0179-0.00350.0881-0.00020.0014-0.0004-0.00090.00090.00020.00230.0017-0.00070.00980.0012-0.00080.0087-0.00560.0043-2.582417.449728.9564
120.03740.08510.0090.0049-0.03330.0323-0.00040.00030.0010.00170.0011-0.0032-0.00190.0008-0.00070.0032-0.0040.00190.0027-0.0006-0.008518.433111.410822.1858
130.0479-0.47670.03460.0001-0.60170.46470.00040.004-0.00770.00370.0069-0.0216-0.00840.0014-0.00740.01060.00050.01960.03480.0126-0.067618.61543.062811.8986
140.0369-0.15740.12950-0.15950.2103-0.00050.00140.0045-0.007200.0038-0.00630.00060.0006-0.00010.01230.00440.01210.0111-0.02014.130110.290112.5877
150.5057-0.11910.51990.0312-0.00010.3796-0.0024-0.01420.0135-0.00130.0002-0.0043-0.0008-0.00640.00230.01410.00730.00710.03920.0102-0.062910.12075.70663.8374
160.17630.3420.197900.13820.17320.00050.00170.0026-0.0003-0.00120.010.0028-0.00030.00070.0175-0.025-0.0040.0261-0.0121-0.05323.5613-1.68855.0006
170.04620.26980.049400.0540.2273-0.0001-0.0045-0.0045-0.0019-0.00220.00380.0086-0.00120.00220.0279-0.02130.00210.0226-0.0206-0.0616.5394-5.205521.3817
18-0.0011-0.03270.00370.01740.00980.00520.00010.0008-0.00140.00090.0003-0.00080.0004-0.0003-0.00050.00470.00540.00520.0018-0.0037-0.007718.1261-8.19666.5355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|31 - A|43}A31 - 43
2X-RAY DIFFRACTION2{A|44 - A|55}A44 - 55
3X-RAY DIFFRACTION3{A|56 - A|78}A56 - 78
4X-RAY DIFFRACTION4{A|79 - A|116}A79 - 116
5X-RAY DIFFRACTION5{A|117 - A|143}A117 - 143
6X-RAY DIFFRACTION6{A|144 - A|170}A144 - 170
7X-RAY DIFFRACTION7{A|171 - A|206}A171 - 206
8X-RAY DIFFRACTION8{A|207 - A|236}A207 - 236
9X-RAY DIFFRACTION9{A|237 - A|249}A237 - 249
10X-RAY DIFFRACTION10{B|31 - B|43}B31 - 43
11X-RAY DIFFRACTION11{B|44 - B|55}B44 - 55
12X-RAY DIFFRACTION12{B|56 - B|78}B56 - 78
13X-RAY DIFFRACTION13{B|79 - B|116}B79 - 116
14X-RAY DIFFRACTION14{B|117 - B|143}B117 - 143
15X-RAY DIFFRACTION15{B|144 - B|170}B144 - 170
16X-RAY DIFFRACTION16{B|171 - B|206}B171 - 206
17X-RAY DIFFRACTION17{B|207 - B|236}B207 - 236
18X-RAY DIFFRACTION18{B|237 - B|248}B237 - 248

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