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- PDB-6qin: CRYSTAL STRUCTURE OF THE PMGL2 ESTERASE FROM PERMAFROST METAGENOM... -

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Basic information

Entry
Database: PDB / ID: 6qin
TitleCRYSTAL STRUCTURE OF THE PMGL2 ESTERASE 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 / triacylglycerol lipase activity / Alpha/Beta hydrolase fold / PMGL2
Function and homology information
Biological speciespermafrost metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsBoyko, K.M. / 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 21, 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 / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / pdbx_struct_conn_angle / 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 / _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
Revision 1.3Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: PMGL2
B: PMGL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7245
Polymers74,6402
Non-polymers843
Water10,629590
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-32 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.010, 92.350, 74.230
Angle α, β, γ (deg.)90.000, 106.830, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 318
2010B1 - 318

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Components

#1: Protein PMGL2


Mass: 37320.172 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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / 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: 40.47 %
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: Jun 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→56.31 Å / Num. obs: 77747 / % possible obs: 97.4 % / Redundancy: 6.1 % / CC1/2: 0.985 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.061 / Rrim(I) all: 0.153 / Net I/σ(I): 7.8 / Num. measured all: 477406 / Scaling rejects: 813
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.6-1.635.90.65338080.8330.2880.71695.9
8.76-56.3170.1175240.9840.0490.12799.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimless0.5.23data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L1H

3l1h


Resolution: 1.6→56.31 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.659 / SU ML: 0.057 / SU R Cruickshank DPI: 0.0829 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.083
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1866 3883 5 %RANDOM
Rwork0.157 ---
obs0.1585 73837 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.82 Å2 / Biso mean: 18.076 Å2 / Biso min: 7.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å2-0 Å20.82 Å2
2---0.13 Å2-0 Å2
3----0.67 Å2
Refinement stepCycle: final / Resolution: 1.6→56.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4731 0 3 590 5324
Biso mean--17.37 27.94 -
Num. residues----630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0134937
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174564
X-RAY DIFFRACTIONr_angle_refined_deg2.2991.6476722
X-RAY DIFFRACTIONr_angle_other_deg2.1891.56810495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4365628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.74919.255282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62615707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2131559
X-RAY DIFFRACTIONr_chiral_restr0.1210.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.025685
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021154
Refine LS restraints NCS

Ens-ID: 1 / Number: 9851 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 307 -
Rwork0.218 5377 -
all-5684 -
obs--96.11 %

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