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- PDB-7cwq: Crystal structure of a novel cutinase from Burkhoderiales bacteri... -

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Basic information

Entry
Database: PDB / ID: 7cwq
TitleCrystal structure of a novel cutinase from Burkhoderiales bacterium RIFCSPLOWO2_02_FULL_57_36
ComponentsDLH domain-containing protein
KeywordsHYDROLASE / substrate binding / inhibitor
Function / homologyDienelactone hydrolase / Dienelactone hydrolase family / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / Dienelactone hydrolase domain-containing protein
Function and homology information
Biological speciesBurkholderiales bacterium RIFCSPLOWO2_02_FULL_57_36 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHan, X. / Liu, W.D. / Zheng, Y.Y. / Chen, C.C. / Guo, R.T.
CitationJournal: Nat Catal / Year: 2021
Title: General features to enhance enzymatic activity of poly(ethylene terephthalate) hydrolysis.
Authors: Che, C.C. / Han, X. / Li, X. / Jiang, P. / Niu, D. / Ma, L. / Liu, W. / Li, S. / Qu, Y. / Hu, H. / Min, J. / Yang, Y. / Zhang, L. / Zeng, W. / Huang, J.W. / Dai, L. / Guo, R.T.
History
DepositionAug 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct.title
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 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: DLH domain-containing protein
B: DLH domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3696
Polymers57,9852
Non-polymers3844
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-55 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.967, 69.967, 381.890
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein DLH domain-containing protein


Mass: 28992.307 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderiales bacterium RIFCSPLOWO2_02_FULL_57_36 (bacteria)
Gene: A3I66_11710 / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1F4JXW8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.34 Å3/Da / Density % sol: 47.41 % / Mosaicity: 0.61 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: Polyethylene Glycol 6000, Glycerol, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 29, 2019
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→25 Å / Num. obs: 68361 / % possible obs: 100 % / Redundancy: 30.3 % / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.11 / Rrim(I) all: 0.214 / Χ2: 1.033 / Net I/σ(I): 3.3 / Num. measured all: 2071637
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Χ2Rpim(I) allRmerge(I) obsRrim(I) all
1.65-1.7113.566890.7790.517
1.71-1.7815.766570.8870.5340.636
1.78-1.8619.966690.9370.5570.424
1.86-1.9625.567310.9650.5910.336
1.96-2.0831.867180.9850.650.242
2.08-2.2435.167550.9910.710.199
2.24-2.4641.668060.9940.7510.248
2.46-2.8243.268670.9960.8530.154
2.82-3.5540.369920.9971.4350.0530.3370.341
3.55-2534.874770.9982.6060.0230.1320.134

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XFY

5xfy


Resolution: 1.65→24.89 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.715 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1955 3381 5 %RANDOM
Rwork0.1648 ---
obs0.1663 64801 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.51 Å2 / Biso mean: 14.978 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.06 Å2-0 Å2
2---0.11 Å20 Å2
3---0.36 Å2
Refinement stepCycle: final / Resolution: 1.65→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4074 0 20 530 4624
Biso mean--32.59 28.26 -
Num. residues----540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134214
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173752
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.6535772
X-RAY DIFFRACTIONr_angle_other_deg1.4711.5688682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7455538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33722.527182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3415608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5461518
X-RAY DIFFRACTIONr_chiral_restr0.0860.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024850
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02956
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 244 -
Rwork0.24 4602 -
all-4846 -
obs--98.68 %

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