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- PDB-7b4q: Structure of a cold active HSL family esterase reveals mechanisms... -

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Basic information

Entry
Database: PDB / ID: 7b4q
TitleStructure of a cold active HSL family esterase reveals mechanisms of low temperature adaptation and substrate specificity
ComponentsLipase
KeywordsHYDROLASE / Bacillus cohnii / esterase / low temperature adapted / regio-selective esterase / Hormone-sensitive family / lipase
Function / homology: / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / triacylglycerol lipase / triacylglycerol lipase activity / Alpha/Beta hydrolase fold / DI(HYDROXYETHYL)ETHER / Lipase
Function and homology information
Biological speciesBacillus cohnii NBRC 15565 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsRizkallah, P.J. / Jones, D.D. / Noby, N. / Auhim, H.
CitationJournal: Open Biology / Year: 2021
Title: Structure and in silico simulations of a cold-active esterase reveals its prime cold-adaptation mechanism.
Authors: Noby, N. / Auhim, H.S. / Winter, S. / Worthy, H.L. / Embaby, A.M. / Saeed, H. / Hussein, A. / Pudney, C.R. / Rizkallah, P.J. / Wells, S.A. / Jones, D.D.
History
DepositionDec 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 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: Lipase
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5359
Polymers71,0652
Non-polymers4717
Water10,521584
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint13 kcal/mol
Surface area25540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.883, 109.883, 126.772
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-740-

HOH

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: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 1 - 314 / Label seq-ID: 1 - 314

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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lipase


Mass: 35532.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cohnii NBRC 15565 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2K9UV39, triacylglycerol lipase

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Non-polymers , 5 types, 591 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2M lithium chloride, 0.1M sodium acetate, 20% (w/v) PEG 6000, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97629 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97629 Å / Relative weight: 1
ReflectionResolution: 1.61→83.04 Å / Num. obs: 100631 / % possible obs: 100 % / Redundancy: 14.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.029 / Rrim(I) all: 0.11 / Net I/σ(I): 13.8 / Num. measured all: 1459945 / Scaling rejects: 1385
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
1.61-1.6513.72.2610034173390.6720.6342.3491100
7.2-83.0413.40.0381752213090.9990.0110.0440.399.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LZK

1lzk


Resolution: 1.61→83.03 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1903 / WRfactor Rwork: 0.162 / FOM work R set: 0.8489 / SU B: 3.541 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0758 / SU Rfree: 0.0766 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1932 5029 5 %RANDOM
Rwork0.1671 ---
obs0.1683 95500 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.78 Å2 / Biso mean: 30.793 Å2 / Biso min: 12.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.25 Å2
Refinement stepCycle: final / Resolution: 1.61→83.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4886 0 30 584 5500
Biso mean--44.5 40.14 -
Num. residues----628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135145
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174811
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.6487015
X-RAY DIFFRACTIONr_angle_other_deg1.5131.5811123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6115652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45822.836275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.115824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3981533
X-RAY DIFFRACTIONr_chiral_restr0.0950.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025939
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021123
Refine LS restraints NCS

Ens-ID: 1 / Number: 10174 / 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: 1.61→1.651 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 395 -
Rwork0.288 6897 -
all-7292 -
obs--99.4 %
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)
11.77270.0618-1.10111.34210.00521.9147-0.0879-0.0132-0.0927-0.00790.00890.13250.11040.00660.0790.01080.00730.00720.01210.00560.020213.635833.389542.9796
21.76670.1263-0.48891.53550.05412.2449-0.0562-0.0262-0.1774-0.06960.001-0.21520.20140.31720.05520.02760.0440.02710.08590.03380.065744.289931.843223.7337
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 314
2X-RAY DIFFRACTION2B1 - 314

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