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- PDB-7e30: Crystal structure of a novel alpha/beta hydrolase in apo form in ... -

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Basic information

Entry
Database: PDB / ID: 7.0E+30
TitleCrystal structure of a novel alpha/beta hydrolase in apo form in complex with citrate
Componentsalpha/beta hydrolase
KeywordsHYDROLASE / alpha/beta dehydrogenase
Function / homologyCITRIC ACID
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpha/beta hydrolase
B: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4478
Polymers55,7082
Non-polymers7396
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-77 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.974, 97.086, 99.112
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
11(chain A and (resid 1 through 258 or resid 401))
21(chain B and (resid 1 through 258 or resid 401))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 258 or resid 401))A0
211(chain B and (resid 1 through 258 or resid 401))B0

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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.) unidentified (others) / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.11 % / Mosaicity: 0.353 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: MPD, PEG 1500, 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: 1.56→25 Å / Num. obs: 77551 / % possible obs: 99.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.036 / Rrim(I) all: 0.084 / Χ2: 1.026 / Net I/σ(I): 17.1 / Num. measured all: 384676
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.56-1.623.20.475860.8380.2660.4841.03399.6
1.62-1.683.50.32476860.9110.20.3841.08599.9
1.68-1.764.10.25676910.9410.1440.2951.10399.9
1.76-1.854.80.20376500.9690.1020.2281.184100
1.85-1.975.70.15577090.9850.0710.1711.261100
1.97-2.125.70.1177140.9910.0510.1211.161100
2.12-2.335.70.08577460.9940.0390.0941.01499.9
2.33-2.675.70.07277900.9950.0330.0790.92100
2.67-3.365.80.0678450.9960.0270.0660.77100
3.36-255.50.06481340.9950.0290.0710.83299.8

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Processing

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

5zrq


Resolution: 1.56→24.55 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1712 3866 4.99 %
Rwork0.1494 73583 -
obs0.1504 77449 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.5 Å2 / Biso mean: 20.1243 Å2 / Biso min: 8.56 Å2
Refinement stepCycle: final / Resolution: 1.56→24.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 0 47 555 4526
Biso mean--32.35 32.03 -
Num. residues----516
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1582X-RAY DIFFRACTION6.844TORSIONAL
12B1582X-RAY DIFFRACTION6.844TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.56-1.620.22323730.199672087581
1.62-1.680.2163910.180172967687
1.68-1.760.20483860.164472897675
1.76-1.850.1793830.152272617644
1.85-1.970.17293790.148173227701
1.97-2.120.17433900.141673207710
2.12-2.330.17933870.141173547741
2.33-2.670.18883850.149873957780
2.67-3.360.16553910.148874387829
3.36-24.550.14634010.142977008101

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