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- PDB-3wyn: Structure of calcium bound cutinase Est119 from Thermobifida alba. -

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Basic information

Entry
Database: PDB / ID: 3wyn
TitleStructure of calcium bound cutinase Est119 from Thermobifida alba.
ComponentsEsterase
KeywordsHYDROLASE / alpha/beta-hydrolase fold / esterase / polyethylene terephthalate
Function / homology
Function and homology information


poly(ethylene terephthalate) hydrolase / cutinase activity / cutinase / periplasmic space / extracellular region / metal ion binding
Similarity search - Function
Cutinase / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsKitadokoro, K. / Thumarat, U. / Kawai, F.
CitationJournal: To be Published
Title: Structure of calcium bound cutinase Est119 from Thermobifida alba.
Authors: Kitadokoro, K. / Thumarat, U. / Kawai, F.
History
DepositionSep 2, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)66,9656
Polymers66,4302
Non-polymers5354
Water7,656425
1
A: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2552
Polymers33,2151
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7104
Polymers33,2151
Non-polymers4953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.473, 87.740, 72.619
Angle α, β, γ (deg.)90.00, 133.35, 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 425 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 25% (w/v) PEG 3000, 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: Oct 12, 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: 1.68→50 Å / Num. all: 51435 / Num. obs: 48769 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.057
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 15 / Num. unique all: 5004 / % possible all: 96.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VIS

3vis


Resolution: 1.68→31.26 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.327 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 2609 5.1 %RANDOM
Rwork0.19588 ---
all0.19797 51435 --
obs0.19797 48769 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.837 Å2
Baniso -1Baniso -2Baniso -3
1--2.82 Å20 Å2-2.36 Å2
2---0.65 Å20 Å2
3---2.05 Å2
Refinement stepCycle: LAST / Resolution: 1.68→31.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 27 425 4464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0194138
X-RAY DIFFRACTIONr_angle_refined_deg2.4161.9585629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2665518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70222.787183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08215624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1851536
X-RAY DIFFRACTIONr_chiral_restr0.1650.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213202
LS refinement shellResolution: 1.681→1.725 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 155 -
Rwork0.375 3080 -
obs--83.57 %
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)
10.27790.06450.26640.3604-0.03540.2837-0.02330.00490.0009-0.03160.0144-0.0099-0.01010.00520.00890.0315-0.00130.03970.06360.00210.05523.2598-26.584323.7553
20.3214-0.01120.46220.3423-0.14750.8175-0.03040.00380.01020.01390.00980.0028-0.04510.04020.02060.0217-0.00430.02450.0428-0.00240.035421.9594-0.3963.0262
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 300
2X-RAY DIFFRACTION2B40 - 300

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