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- PDB-4eb0: Crystal structure of Leaf-branch compost bacterial cutinase homolog -

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Basic information

Entry
Database: PDB / ID: 4eb0
TitleCrystal structure of Leaf-branch compost bacterial cutinase homolog
ComponentsLCC
KeywordsHYDROLASE / Serine esterase / Cutinase homolog / PET degradation / Metagenome
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / cutinase / cutinase activity / extracellular region
Similarity search - Function
Alpha/beta hydrolase family / 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
THIOCYANATE ION / Leaf-branch compost cutinase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSulaiman, S. / You, D.J. / Eiko, K. / Koga, Y. / Kanaya, S.
CitationJournal: To be Published
Title: Crystal structure of Leaf-branch compost bacterial cutinase homolog
Authors: Sulaiman, S. / You, D.J. / Eiko, K. / Koga, Y. / Kanaya, S.
History
DepositionMar 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 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 / 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0325
Polymers27,8001
Non-polymers2324
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.911, 71.084, 72.726
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 LCC


Mass: 27799.992 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 36-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RP / References: UniProt: G9BY57, cutinase
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.33 % / Mosaicity: 0.651 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% (w/v) polyethylene glycol (PEG) 3350, 200mM sodium thiocyanate, pH 7.0, 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: BRUKER SMART 6500 / Detector: CCD / Date: Oct 10, 2011
RadiationMonochromator: horizontal focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 35110 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Χ2: 1.034 / Net I/σ(I): 31.657
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
1.5-1.5312.70.4190.41917420.4190.362100
1.53-1.5513.30.40617310.373100
1.55-1.5813.60.37617120.406100
1.58-1.6213.90.34417250.436100
1.62-1.6514.10.32317230.461100
1.65-1.6914.20.2917190.508100
1.69-1.7314.30.2717440.535100
1.73-1.7814.30.24617490.606100
1.78-1.8314.30.21717130.696100
1.83-1.8914.20.19317520.819100
1.89-1.9614.30.18417510.933100
1.96-2.0414.10.16517371.08699.9
2.04-2.13140.15117431.21100
2.13-2.24140.14617501.381100
2.24-2.3813.90.14517711.672100
2.38-2.5613.60.14517652.07299.9
2.56-2.8213.20.14117562.38199.9
2.82-3.2312.90.1117912.16399.8
3.23-4.0712.80.06618191.43899.8
4.07-5012.70.05419171.19499.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.72 Å50.84 Å
Translation1.72 Å50.84 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 35051
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.42-10021.50.782508
5.03-6.4221.60.888525
4.27-5.0316.50.924612
3.78-4.2715.20.926691
3.42-3.7819.10.9768
3.15-3.4218.90.897840
2.94-3.1519.90.883896
2.76-2.9418.90.887972
2.61-2.7620.80.892998
2.49-2.61210.8851065
2.38-2.4919.60.8931116
2.28-2.3818.60.9041151
2.19-2.2818.60.9021211
2.12-2.1920.10.8851250
2.05-2.1218.40.8911270
1.99-2.0518.90.8921335
1.93-1.9920.60.8931367
1.88-1.9319.70.9051404
1.83-1.8821.50.9041436
1.78-1.8320.70.9021457
1.74-1.7821.10.9021506
1.7-1.7423.20.9031556
1.66-1.723.20.91579
1.63-1.6623.90.9051603
1.6-1.6324.80.9041658
1.57-1.624.60.9021655
1.54-1.5727.80.9091710
1.49-1.5435.30.8832912

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
DM6.1phasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JFR

1jfr


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.189 / WRfactor Rwork: 0.153 / SU B: 1.126 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1863 1741 5 %RANDOM
Rwork0.15654 ---
obs0.15801 32818 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.41 Å2 / Biso mean: 17.172 Å2 / Biso min: 8.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2---0.04 Å2-0 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 12 315 2289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222023
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg11.9412764
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4295257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30422.75987
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.8415283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0621516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.020.0211578
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4661.51298
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.17522088
X-RAY DIFFRACTIONr_scbond_it3.3983725
X-RAY DIFFRACTIONr_scangle_it4.4584.5676
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 127 -
Rwork0.188 2374 -
obs--99.64 %

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