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- PDB-3vis: Crystal structure of cutinase Est119 from Thermobifida alba AHK119 -

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Basic information

Entry
Database: PDB / ID: 3vis
TitleCrystal structure of cutinase Est119 from Thermobifida alba AHK119
ComponentsEsterase
KeywordsHYDROLASE / alpha/beta-hydrolase fold / esterase / polyethylene terephthalate
Function / homology
Function and homology information


poly(ethylene terephthalate) hydrolase / cutinase / cutinase activity / periplasmic space / extracellular region / metal ion binding
Similarity search - Function
Cutinase / PET hydrolase-like / : / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermobifida alba (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, molecular replacement / Resolution: 1.76 Å
AuthorsKitadokoro, K. / Thumarat, U. / Nakamura, R. / Nishimura, K. / Karatani, H. / Suzuki, H. / Kawai, F.
CitationJournal: POLYM.DEGRAD.STAB. / Year: 2012
Title: Crystal structure of cutinase Est119 from Thermobida alba AHK119 that can degrade modpolyethylene terephthalate at 1.76 A resolution.
Authors: Kitadokoro, K. / Thumarat, U. / Nakamura, R. / Nishimura, K. / Karatani, H. / Suzuki, H. / Kawai, F.
History
DepositionOct 11, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Esterase
B: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7853
Polymers66,4302
Non-polymers3541
Water8,179454
1
A: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5702
Polymers33,2151
Non-polymers3541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Esterase


Theoretical massNumber of molelcules
Total (without water)33,2151
Polymers33,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.989, 88.732, 71.794
Angle α, β, γ (deg.)90.00, 133.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Esterase


Mass: 33215.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida alba (bacteria) / Strain: AHK119 / Gene: est2 / Plasmid: pQE80L-est119 / Production host: Escherichia coli (E. coli) / References: UniProt: F7IX06
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 25% (w/v) PEG 1000, 0.2M sodium chloride, 0.1M sodium potassium phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 24, 2011 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.76→56.8 Å / Num. all: 44072 / Num. obs: 41770 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.099
Reflection shellResolution: 1.76→1.82 Å / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.6.0081refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD, molecular replacement / Resolution: 1.76→56.75 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.559 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19615 2222 5.1 %RANDOM
Rwork0.14997 ---
obs0.15237 41770 96.32 %-
all-43992 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.825 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å20 Å2-2.09 Å2
2---1.38 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.76→56.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4020 0 24 454 4498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0224146
X-RAY DIFFRACTIONr_angle_refined_deg2.1741.9595640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9275519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.64222.787183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31815626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7671536
X-RAY DIFFRACTIONr_chiral_restr0.1750.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213206
LS refinement shellResolution: 1.762→1.808 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 142 -
Rwork0.19 2955 -
obs--92.31 %
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)
10.51960.03880.32260.8506-0.00640.3642-0.0339-0.00820.0054-0.08310.0214-0.0317-0.0103-0.01060.01250.0322-0.00730.0340.05260.00530.04923.4905-26.783523.6601
20.56720.02090.64870.4682-0.0081.1984-0.02240.00140.0064-0.03960.04690.0301-0.01020.0321-0.02450.0164-0.00790.00830.02250.00610.022822.3826-0.67782.7135
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 300
2X-RAY DIFFRACTION2B40 - 300

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