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- PDB-7b1x: Crystal structure of cold-active esterase PMGL3 from permafrost m... -

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Basic information

Entry
Database: PDB / ID: 7b1x
TitleCrystal structure of cold-active esterase PMGL3 from permafrost metagenomic library
Componentsesterase PMGL3
KeywordsHYDROLASE / esterase / HSL / permafrost / cold-active / psychrophilic / tetramer / dimer / lipase
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Petrovskaya, L.E. / Kryukova, M.V. / Kryukova, E.A. / Korzhenevsky, D.A. / Lomakina, G.Y. / Novototskaya-Vlasova, K.A. / Rivkina, E.M. / Dolgikh, D.A. ...Boyko, K.M. / Nikolaeva, A.Y. / Petrovskaya, L.E. / Kryukova, M.V. / Kryukova, E.A. / Korzhenevsky, D.A. / Lomakina, G.Y. / 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: Biomolecules / Year: 2021
Title: Structural and Biochemical Characterization of a Cold-Active PMGL3 Esterase with Unusual Oligomeric Structure.
Authors: Boyko, K.M. / Kryukova, M.V. / Petrovskaya, L.E. / Kryukova, E.A. / Nikolaeva, A.Y. / Korzhenevsky, D.A. / Lomakina, G.Y. / Novototskaya-Vlasova, K.A. / Rivkina, E.M. / Dolgikh, D.A. / ...Authors: Boyko, K.M. / Kryukova, M.V. / Petrovskaya, L.E. / Kryukova, E.A. / Nikolaeva, A.Y. / Korzhenevsky, D.A. / Lomakina, G.Y. / Novototskaya-Vlasova, K.A. / Rivkina, E.M. / Dolgikh, D.A. / Kirpichnikov, M.P. / Popov, V.O.
History
DepositionNov 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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: esterase PMGL3
B: esterase PMGL3


Theoretical massNumber of molelcules
Total (without water)66,8812
Polymers66,8812
Non-polymers00
Water3,549197
1
A: esterase PMGL3
B: esterase PMGL3

A: esterase PMGL3
B: esterase PMGL3


Theoretical massNumber of molelcules
Total (without water)133,7634
Polymers133,7634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6560 Å2
ΔGint-26 kcal/mol
Surface area41930 Å2
MethodPISA
2
A: esterase PMGL3

A: esterase PMGL3

B: esterase PMGL3

B: esterase PMGL3


Theoretical massNumber of molelcules
Total (without water)133,7634
Polymers133,7634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_556-x,y,-z+11
Buried area4610 Å2
ΔGint-33 kcal/mol
Surface area43880 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-8 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.800, 98.400, 75.200
Angle α, β, γ (deg.)90.000, 128.100, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 302 / Label seq-ID: 1 - 302

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

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Components

#1: Protein esterase PMGL3


Mass: 33440.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: triacylglycerol lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 288 K / Method: vapor diffusion
Details: 0.1M Sodium citrate tribasic dihydrate pH 5.6; 20% isopropanol; 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.1→37.28 Å / Num. obs: 33658 / % possible obs: 96.2 % / Redundancy: 6.034 % / Biso Wilson estimate: 44.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.118 / Χ2: 0.94 / Net I/σ(I): 14.58 / Num. measured all: 203107 / Scaling rejects: 80
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.22.2630.5291.5441360.6610.68691.7
2.2-2.54.0230.623.190200.8570.68893.5
2.5-37.6650.3867.7885760.9660.41498.5
3-47.5670.123.6968530.9970.10898.5
4-107.9090.0544.1947370.9980.05498.6
10-507.1790.0553.393360.9980.05396.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FAK

3fak


Resolution: 2.3→37.28 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.929 / SU B: 15.695 / SU ML: 0.182 / SU R Cruickshank DPI: 0.4503 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.45 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 1182 5 %RANDOM
Rwork0.1615 ---
obs0.1649 22446 89.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.25 Å2 / Biso mean: 41.741 Å2 / Biso min: 20.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20.2 Å2
2--1.32 Å20 Å2
3----0.95 Å2
Refinement stepCycle: final / Resolution: 2.3→37.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4507 0 0 197 4704
Biso mean---40.65 -
Num. residues----604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124632
X-RAY DIFFRACTIONr_angle_refined_deg2.0741.6226310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1095602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5421.957230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.57815684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1751530
X-RAY DIFFRACTIONr_chiral_restr0.1460.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023620
Refine LS restraints NCS

Ens-ID: 1 / Number: 9755 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 98 -
Rwork0.241 1666 -
all-1764 -
obs--91.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.22370.01320.10460.51970.03070.79710.06370.33870.03840.00180.0082-0.04370.09370.0167-0.07190.06910.032-0.020.1510.01180.0154-29.11980.68535.0134
20.9504-0.01050.03180.53540.05940.79490.0493-0.0740.22190.02270.01160.0235-0.0213-0.2404-0.06090.0230.02810.00090.1104-0.00550.1001-48.446115.16229.6386
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 302
2X-RAY DIFFRACTION2B1 - 302

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