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

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Basic information

Entry
Database: PDB / ID: 7cuv
TitleCrystal structure of a novel alpha/beta hydrolase in apo form
Componentsalpha/beta hydrolase
KeywordsHYDROLASE / alpha/beta dehydrogenase
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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
DepositionAug 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: 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 / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)55,7082
Polymers55,7082
Non-polymers00
Water11,710650
1
A: alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)27,8541
Polymers27,8541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)27,8541
Polymers27,8541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.010, 69.541, 74.853
Angle α, β, γ (deg.)90.000, 102.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein alpha/beta hydrolase


Mass: 27853.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 2.37 Å3/Da / Density % sol: 48.17 % / Mosaicity: 0.749 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: MPD, PEG1500, 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 PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2019
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→25 Å / Num. obs: 89271 / % possible obs: 96.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.065 / Rrim(I) all: 0.185 / Χ2: 1.4 / Net I/σ(I): 8.3 / Num. measured all: 605037
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.53.80.46385500.8720.2490.5280.53993.5
1.5-1.564.50.4588110.9120.2180.5020.60396.3
1.56-1.635.50.50589120.9360.2210.5530.6896.7
1.63-1.726.80.54688890.9450.2160.5880.76997.1
1.72-1.837.70.44489480.9680.1670.4741.04597.4
1.83-1.977.70.40390240.9720.1490.431.50997.8
1.97-2.178.40.24190630.9820.0870.2561.5898.4
2.17-2.487.30.1989100.9810.0720.2041.97596.4
2.48-3.128.30.1491680.9870.0510.1492.16699.4
3.12-257.30.12389960.9870.0470.1321.84695.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZRQ

5zrq


Resolution: 1.45→23 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1775 4457 5 %
Rwork0.1594 84700 -
obs0.1603 89157 96.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.02 Å2 / Biso mean: 18.3633 Å2 / Biso min: 8.44 Å2
Refinement stepCycle: final / Resolution: 1.45→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3912 0 0 650 4562
Biso mean---31.08 -
Num. residues----514
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 (%)
1.45-1.50.24194190.20967964838391
1.5-1.560.21314410.18118374881596
1.56-1.630.19824450.16738466891197
1.63-1.720.20494460.1638452889897
1.72-1.830.17994470.15648507895497
1.83-1.970.18254500.16038584903498
1.97-2.170.17034540.15298613906798
2.17-2.480.17734460.16018473891996
2.48-3.120.17814600.16168724918499
3.12-230.16034490.15138543899296

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