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- PDB-3esd: cut-2b; NCN-Pt-Pincer-Cutinase Hybrid -

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Basic information

Entry
Database: PDB / ID: 3esd
Titlecut-2b; NCN-Pt-Pincer-Cutinase Hybrid
ComponentsCutinase 1
KeywordsHYDROLASE / protein-metallopincer complex / Glycoprotein / Secreted / Serine esterase
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
Chem-SXC / Cutinase 1
Similarity search - Component
Biological speciesFusarium solani f. pisi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsRutten, L. / Mannie, J.P.B.A. / Lutz, M. / Gros, P.
CitationJournal: Chemistry / Year: 2009
Title: Solid-state structural characterization of cutinase-ECE-pincer-metal hybrids
Authors: Rutten, L. / Wieczorek, B. / Mannie, J.P.B.A. / Kruithof, C.A. / Dijkstra, H.P. / Egmond, M.R. / Lutz, M. / Klein Gebbink, R.J.M. / Gros, P. / van Koten, G.
History
DepositionOct 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 9, 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: Cutinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9492
Polymers22,2941
Non-polymers6551
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.360, 72.360, 110.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-284-

HOH

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Components

#1: Protein Cutinase 1 / Cutin hydrolase 1


Mass: 22294.031 Da / Num. of mol.: 1 / Mutation: N172K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium solani f. pisi (fungus) / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00590, cutinase
#2: Chemical ChemComp-SXC / bromo(4-{3-[(R)-ethoxy(4-nitrophenoxy)phosphoryl]propyl}-2,6-bis[(methylsulfanyl-kappaS)methyl]phenyl-kappaC~1~)palladium(2+) / ethyl 4-nitrophenyl P-[3-(4-(bromopallado)-1,3-bis[(methylthio)methyl]-phenyl)propyl]phosphonate


Mass: 654.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27BrNO5PPdS2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEE REFERENCE 2 IN UNIPROT DATABASE P00590

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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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5
Details: 6%(w/v) PEG-3350, 30%(v/v) glycerol, 0.05M BisTrisP, 0.1M potassium thiocyanate, pH 8.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.22→41 Å / Num. obs: 61949 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.7
Reflection shellResolution: 1.22→1.29 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 1.2 / Num. unique all: 7679 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
SHELXL-97refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CUA

1cua


Resolution: 1.22→41 Å / σ(F): 0 / σ(I): 0
Details: Twinning was observed in the present crystal and refined with SHELXL using the TWIN instruction, resulting in a twin fraction of 0.5, operator h,-h-k,-l. The point group 3 of the crystal ...Details: Twinning was observed in the present crystal and refined with SHELXL using the TWIN instruction, resulting in a twin fraction of 0.5, operator h,-h-k,-l. The point group 3 of the crystal lattice can be obtained via a coset decomposition of point group 32 of the twin lattice. The twofold twin axis cannot be a real crystallographic operation because this would result in only half a molecule in the asymmetric unit.
RfactorNum. reflection% reflection
Rfree0.222 --
Rwork0.199 --
all-61949 -
obs-61949 97.1 %
Refinement stepCycle: LAST / Resolution: 1.22→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 22 73 1525
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.04

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