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- PDB-7e31: Crystal structure of a novel alpha/beta hydrolase mutant in apo form -

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Basic information

Entry
Database: PDB / ID: 7.0E+31
TitleCrystal structure of a novel alpha/beta hydrolase mutant in apo form
Componentsalpha/beta hydrolase
KeywordsHYDROLASE / alpha/beta dehydrogenase
Function / homologyTRIETHYLENE GLYCOL
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsGao, J. / Han, X. / Zheng, Y.Y. / Liu, W.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2022
Title: Multiple Substrate Binding Mode-Guided Engineering of a Thermophilic PET Hydrolase.
Authors: Pfaff, L. / Gao, J. / Li, Z. / Jackering, A. / Weber, G. / Mican, J. / Chen, Y. / Dong, W. / Han, X. / Feiler, C.G. / Ao, Y.F. / Badenhorst, C.P.S. / Bednar, D. / Palm, G.J. / Lammers, M. / ...Authors: Pfaff, L. / Gao, J. / Li, Z. / Jackering, A. / Weber, G. / Mican, J. / Chen, Y. / Dong, W. / Han, X. / Feiler, C.G. / Ao, Y.F. / Badenhorst, C.P.S. / Bednar, D. / Palm, G.J. / Lammers, M. / Damborsky, J. / Strodel, B. / Liu, W. / Bornscheuer, U.T. / Wei, R.
History
DepositionFeb 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 30, 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: alpha/beta hydrolase
B: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1584
Polymers55,8582
Non-polymers3002
Water13,926773
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint7 kcal/mol
Surface area18670 Å2
Unit cell
Length a, b, c (Å)55.343, 94.865, 105.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 1 - 258 / Label seq-ID: 1 - 258

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein alpha/beta hydrolase


Mass: 27928.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.48 Å3/Da / Density % sol: 50.38 % / Mosaicity: 0.83 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: MPD, PEG1 500, NaAc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 20, 2020
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→25 Å / Num. obs: 114533 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.019 / Rrim(I) all: 0.056 / Χ2: 1.584 / Net I/σ(I): 18.4 / Num. measured all: 862668
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.38-1.434.30.459113160.8290.2490.5240.685100
1.43-1.494.90.348113540.9030.1750.3910.752100
1.49-1.555.60.244113350.9560.1130.2690.878100
1.55-1.646.60.181113670.9790.0760.1960.974100
1.64-1.748.20.136113490.9910.050.1451.16100
1.74-1.879.30.097113970.9950.0340.1031.369100
1.87-2.069.30.068114320.9970.0240.0721.695100
2.06-2.369.10.053114730.9980.0180.0562.098100
2.36-2.979.40.039115860.9990.0130.0411.879100
2.97-258.60.042119240.9980.0160.0452.84599.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZRQ

5zrq


Resolution: 1.38→24.5 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1752 5721 5 %
Rwork0.1648 108701 -
obs0.1653 114422 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.44 Å2 / Biso mean: 17.1473 Å2 / Biso min: 4.79 Å2
Refinement stepCycle: final / Resolution: 1.38→24.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 20 773 4729
Biso mean--29.84 29.75 -
Num. residues----516
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1592X-RAY DIFFRACTION6.054TORSIONAL
12B1592X-RAY DIFFRACTION6.054TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.38-1.430.24235570.2235106001115798
1.43-1.490.22735670.20311077811345100
1.49-1.550.20715680.18281078511353100
1.55-1.640.19175690.17311081711386100
1.64-1.740.18585680.16741078811356100
1.74-1.870.17575710.16661083311404100
1.87-2.060.17765720.15821088511457100
2.06-2.360.17665740.15591090511479100
2.36-2.970.17025800.16421099811578100
2.97-24.50.15845950.15771131211907100

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