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- PDB-2czq: A novel cutinase-like protein from Cryptococcus sp. -

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Basic information

Entry
Database: PDB / ID: 2czq
TitleA novel cutinase-like protein from Cryptococcus sp.
Componentscutinase-like protein
KeywordsHYDROLASE / alpha/beta hydrolase fold
Function / homology
Function and homology information


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
CITRIC ACID / Cutinase-like enzyme
Similarity search - Component
Biological speciesCryptococcus sp. (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.05 Å
AuthorsMasaki, K. / Kamini, N.R. / Ikeda, H. / Iefuji, H. / Kondo, H. / Suzuki, M. / Tsuda, S.
Citation
Journal: Proteins / Year: 2009
Title: Crystal structure and enhanced activity of a cutinase-like enzyme from Cryptococcus sp. strain S-2
Authors: Kodama, Y. / Masaki, K. / Kondo, H. / Suzuki, M. / Tsuda, S. / Nagura, T. / Shimba, N. / Suzuki, E. / Iefuji, H.
#1: Journal: Appl.Environ.Microbiol. / Year: 2005
Title: Cutinase-like enzyme from the yeast Cryptococcus sp. strain S-2 hydrolyzes polylactic acid and other biodegradable plastics
Authors: Masaki, K. / Kamini, N.R. / Ikeda, H. / Iefuji, H.
#2: Journal: Appl.Microbiol.Biotechnol. / Year: 2012
Title: Construction of a new recombinant protein expression system in the basidiomycetous yeast Cryptococcus sp. strain S-2 and enhancement of the production of a cutinase-like enzyme
Authors: Masaki, K. / Tsuchioka, H. / Hirano, T. / Kato, M. / Ikeda, H. / Iefuji, H.
History
DepositionJul 14, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jun 13, 2012Group: Database references
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cutinase-like protein
B: cutinase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3686
Polymers41,8602
Non-polymers5084
Water7,386410
1
A: cutinase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1843
Polymers20,9301
Non-polymers2542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cutinase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1843
Polymers20,9301
Non-polymers2542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.478, 82.807, 123.514
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 cutinase-like protein


Mass: 20930.057 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cryptococcus sp. (fungus) / Strain: S-2
References: UniProt: Q874E9, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.10541 Å3/Da / Density % sol: 41.579067 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.9
Details: 1.3-1.6M Sodium citrate, pH 5.9, VAPOR DIFFUSION, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A10.978
SYNCHROTRONPhoton Factory BL-6A21.0717, 1.0723, 0.9779
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDMay 27, 2002Mirror-Monochromator
ADSC QUANTUM 42CCDMay 27, 2002Mirror-Monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Mirror-Monochromator Si(111)SINGLE WAVELENGTHMx-ray1
2Mirror-Monochromator Si(111)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
21.07171
31.07231
40.97791
ReflectionResolution: 1.05→23 Å / Num. all: 157936 / Num. obs: 157936 / % possible obs: 95.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Biso Wilson estimate: 5.364 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.067 / Net I/σ(I): 7.4
Reflection shellResolution: 1.05→1.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.2 / Num. unique all: 19883 / Rsym value: 0.333 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.05→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.15716 15686 9.9 %RANDOM
Rwork0.14746 ---
all0.14843 142150 --
obs0.14843 142150 95.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.543 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 34 410 3382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213095
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1671.944216
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6035410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022372
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.21562
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0760.2304
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.291
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5241.52028
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87823249
X-RAY DIFFRACTIONr_scbond_it1.15731067
X-RAY DIFFRACTIONr_scangle_it1.7344.5964
X-RAY DIFFRACTIONr_rigid_bond_restr0.50223095
X-RAY DIFFRACTIONr_sphericity_free1.5182410
X-RAY DIFFRACTIONr_sphericity_bonded1.32123041
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.261 972
Rwork0.247 8719

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