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- PDB-6qla: CRYSTAL STRUCTURE OF THE PMGL2 ESTERASE (point mutant 1) FROM PER... -

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Basic information

Entry
Database: PDB / ID: 6qla
TitleCRYSTAL STRUCTURE OF THE PMGL2 ESTERASE (point mutant 1) FROM PERMAFROST METAGENOMIC LIBRARY
ComponentsPMGL2
KeywordsHYDROLASE / esterase / permafrost / metagenome / HSL family / GCSAG motif
Function / homologyAlpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / triacylglycerol lipase / triglyceride lipase activity / Alpha/Beta hydrolase fold / Chem-PG6 / PMGL2
Function and homology information
Biological speciespermafrost metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.43 Å
AuthorsBoyko, K.M. / Garsia, D. / Nikolaeva, A.Y. / Korzhenevskiy, D.A. / Kryukova, M.V. / Petrovskaya, L.E. / Novototskaya-Vlasova, K.A. / Rivkina, E.M. / Dolgikh, D.A. / Kirpichnikov, M.P. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-04-00491 Russian Federation
CitationJournal: Plos One / Year: 2020
Title: Crystal structure of PMGL2 esterase from the hormone-sensitive lipase family with GCSAG motif around the catalytic serine.
Authors: Boyko, K.M. / Kryukova, M.V. / Petrovskaya, L.E. / Nikolaeva, A.Y. / Korzhenevsky, D.A. / Novototskaya-Vlasova, K.A. / Rivkina, E.M. / Dolgikh, D.A. / Kirpichnikov, M.P. / Popov, V.O.
History
DepositionJan 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 11, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / pdbx_struct_conn_angle / refine / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.3Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PMGL2
B: PMGL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9969
Polymers75,0892
Non-polymers9077
Water10,395577
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-23 kcal/mol
Surface area23090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.140, 92.180, 74.460
Angle α, β, γ (deg.)90.000, 106.410, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 14 - 332 / Label seq-ID: 14 - 332

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein PMGL2


Mass: 37544.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) permafrost metagenome (others) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A142J6I6, triacylglycerol lipase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE / Polyethylene glycol


Mass: 266.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O6
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 2.07 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 250mM Magnesium chloride, 12-18% PEG3350, 100mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→56.46 Å / Num. obs: 110412 / % possible obs: 98 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.033 / Rrim(I) all: 0.082 / Net I/σ(I): 12.4 / Num. measured all: 654037 / Scaling rejects: 20
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.43-1.455.50.9592879152650.6260.4431.061.895.2
7.82-56.466.70.0348697260.9990.0120.03236.799.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
HKL-2000data reduction
Aimless0.5.31data scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QIN

6qin


Resolution: 1.43→56.46 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1789 / WRfactor Rwork: 0.1514 / FOM work R set: 0.8651 / SU B: 1.201 / SU ML: 0.045 / SU R Cruickshank DPI: 0.059 / SU Rfree: 0.0618 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.184 5606 5.1 %RANDOM
Rwork0.1562 ---
obs0.1576 104774 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.3 Å2 / Biso mean: 18.001 Å2 / Biso min: 7.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å20.49 Å2
2--0.26 Å20 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 1.43→56.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4805 0 49 577 5431
Biso mean--28.09 28.53 -
Num. residues----638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0135060
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174726
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.6496880
X-RAY DIFFRACTIONr_angle_other_deg1.6911.56710877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.75919.123285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39715727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9351561
X-RAY DIFFRACTIONr_chiral_restr0.1030.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025775
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021176
Refine LS restraints NCS

Ens-ID: 1 / Number: 10244 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.428→1.465 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 393 -
Rwork0.295 7502 -
all-7895 -
obs--94.71 %

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