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- PDB-5zoa: The crystal structure of a Thermobifida fusca cutinase -

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Basic information

Entry
Database: PDB / ID: 5zoa
TitleThe crystal structure of a Thermobifida fusca cutinase
ComponentsBTA-hydrolase 1
KeywordsHYDROLASE / cutin / Thermobifida fusca cutinase hydrolysis activity
Function / homology
Function and homology information


poly(ethylene terephthalate) hydrolase / cutinase / cutinase activity / periplasmic space / extracellular region
Similarity search - Function
Chlorophyllase / Chlorophyllase / : / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.537 Å
AuthorsDong, Q.L. / Wu, L. / Wu, J. / Zhou, J.H.
CitationJournal: To Be Published
Title: The crystal structure of a cutinase from Thermobifida fusca
Authors: Dong, Q.L. / Wu, L. / Wu, J. / Zhou, J.H.
History
DepositionApr 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BTA-hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2733
Polymers28,2031
Non-polymers712
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.298, 86.298, 76.117
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422

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Components

#1: Protein BTA-hydrolase 1 / Cutinase


Mass: 28202.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Gene: bta1, cut_2 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q6A0I4, cutinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.0M NaCl, 4.0%(v/v) Polypropylene glycel P400, 0.1M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jan 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.537→50 Å / Num. obs: 43283 / % possible obs: 99.8 % / Redundancy: 18.6 % / Net I/σ(I): 2
Reflection shellResolution: 1.54→1.6 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.537→28.542 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.68
RfactorNum. reflection% reflection
Rfree0.1801 2089 4.83 %
Rwork0.1658 --
obs0.1664 43229 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.537→28.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 2 158 2148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012069
X-RAY DIFFRACTIONf_angle_d1.1472834
X-RAY DIFFRACTIONf_dihedral_angle_d2.7911685
X-RAY DIFFRACTIONf_chiral_restr0.074318
X-RAY DIFFRACTIONf_plane_restr0.008372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5374-1.57310.23871320.21112652X-RAY DIFFRACTION98
1.5731-1.61250.22581390.18412684X-RAY DIFFRACTION100
1.6125-1.65610.16671440.16962695X-RAY DIFFRACTION100
1.6561-1.70480.18431190.15612702X-RAY DIFFRACTION100
1.7048-1.75980.18331310.15462737X-RAY DIFFRACTION100
1.7598-1.82270.20561620.14982704X-RAY DIFFRACTION100
1.8227-1.89560.16391400.15672683X-RAY DIFFRACTION100
1.8956-1.98190.18291040.15682766X-RAY DIFFRACTION100
1.9819-2.08640.16581500.15132710X-RAY DIFFRACTION100
2.0864-2.2170.15951540.15462738X-RAY DIFFRACTION100
2.217-2.38810.16921440.16262749X-RAY DIFFRACTION100
2.3881-2.62830.19851430.17322747X-RAY DIFFRACTION100
2.6283-3.00830.20161510.18422765X-RAY DIFFRACTION100
3.0083-3.78870.16281330.16682840X-RAY DIFFRACTION100
3.7887-28.54730.17971430.1642968X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -15.074 Å / Origin y: 31.7331 Å / Origin z: 17.1818 Å
111213212223313233
T0.0614 Å20.0007 Å20.0134 Å2-0.0815 Å20.0049 Å2--0.0583 Å2
L1.8747 °20.758 °2-0.2088 °2-1.8214 °2-0.1433 °2--1.5125 °2
S-0.0907 Å °-0.0371 Å °-0.0604 Å °-0.0455 Å °0.0439 Å °-0.0109 Å °0.004 Å °0.1548 Å °-0.0111 Å °
Refinement TLS groupSelection details: all

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