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- PDB-7spn: Crystal structure of IS11, a thermophilic esterase -

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Basic information

Entry
Database: PDB / ID: 7spn
TitleCrystal structure of IS11, a thermophilic esterase
ComponentsIS11
KeywordsHYDROLASE / esterase / thermophilic / alpha/beta protein
Function / homologyBeta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / hydrolase activity / Class A beta-lactamase-related serine hydrolase
Function and homology information
Biological speciesDehalococcoidia bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsStogios, P.J. / Evdokimova, E. / Khusnutdinova, A. / Yakunin, A.F. / Savchenko, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of IS11, a thermophilic esterase
Authors: Yakunin, A.F.
History
DepositionNov 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 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

Downloads & links

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Assembly

Deposited unit
A: IS11
B: IS11


Theoretical massNumber of molelcules
Total (without water)98,9552
Polymers98,9552
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-11 kcal/mol
Surface area33640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.216, 103.359, 94.857
Angle α, β, γ (deg.)90.000, 103.481, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein IS11


Mass: 49477.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dehalococcoidia bacterium (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7C2VFT1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1 M citric acid pH 3.5, 19% PEG3350, Cryoprotectant paratone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.92→50 Å / Num. obs: 20309 / % possible obs: 98.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 64.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.069 / Net I/σ(I): 11.95
Reflection shellResolution: 2.92→2.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1004 / CC1/2: 0.572 / Rpim(I) all: 0.528 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2-generated model

Resolution: 2.92→45.09 Å / SU ML: 0.3308 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.9434
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 1834 9.79 %RANDOM
Rwork0.1969 16905 --
obs0.2029 18739 89.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.37 Å2
Refinement stepCycle: LAST / Resolution: 2.92→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6990 0 0 23 7013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00247180
X-RAY DIFFRACTIONf_angle_d0.53449791
X-RAY DIFFRACTIONf_chiral_restr0.04021070
X-RAY DIFFRACTIONf_plane_restr0.00491291
X-RAY DIFFRACTIONf_dihedral_angle_d16.83692585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-2.980.37711040.2968983X-RAY DIFFRACTION67.47
2.98-3.070.37841340.30521148X-RAY DIFFRACTION80.83
3.07-3.170.30761240.28981209X-RAY DIFFRACTION82.28
3.17-3.280.3481320.27161242X-RAY DIFFRACTION87.02
3.28-3.420.33671360.24471281X-RAY DIFFRACTION88.67
3.42-3.570.31861410.24371323X-RAY DIFFRACTION90.37
3.57-3.760.29511420.22151327X-RAY DIFFRACTION93.87
3.76-40.28361470.19421349X-RAY DIFFRACTION92.46
4-4.30.22361510.17261345X-RAY DIFFRACTION93.38
4.3-4.740.21281540.15951414X-RAY DIFFRACTION97.57
4.74-5.420.22591530.16921414X-RAY DIFFRACTION97.75
5.42-6.820.25151570.19431412X-RAY DIFFRACTION96.79
6.83-45.090.2071590.15791458X-RAY DIFFRACTION98
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)
17.841940411724.160341528023.25024282354.555781585683.288234916794.17567086590.1094644225820.3389445964330.7502751968460.546182658344-0.2029593512380.160249562395-0.3047822613720.2056665154620.2031956023190.8138381407960.004516889662240.02905896371970.311413429995-0.01364280712090.475797162578-0.40076328910918.181318232216.463093679
21.28593138882-0.839272493483-0.3237110302311.04671952303-0.1680810014311.63664449010.0018655361889-0.0538012896512-0.208392735140.2288651852290.04456283334260.07735052012060.2196406429680.0448498418486-0.04011454268350.484448733852-0.04435459368530.005896207975460.273636024237-0.007060938717140.4299042340046.96139170776-7.582871335078.98008262103
30.0731395084002-0.1892548437790.1589714646310.1240552932180.08946194700981.71927165809-0.147238465750.0497092544840.120032848412-0.0409454621732-0.04629910578420.255273340143-0.275933376586-0.051908943030.2345408822710.675971175351-0.0177970264590.0405509449960.3836314154810.009856846020490.6239165127635.9301169324710.2471243458-0.520509629448
45.32786461917-0.350032353038-2.642355795011.193841409711.537601719274.02387370089-0.00851048223493-0.0441793399426-0.0526888135637-0.210627468033-0.01348244534430.005905763530430.321722041174-0.4723782032110.04413023554420.55378448281-0.0140605566102-0.1188942707550.4296233603210.1366208271710.426926337021-4.697022627074.57726383541-10.5534859344
58.27298769603-0.4714935598131.235452460076.34470696227-1.318146919961.111752545940.437021544796-0.06652744070660.6581464380320.4291392464110.3698820772970.169197894424-0.7910474804280.0744791385353-0.7338660384631.072278632910.06402054386150.3161351416410.613908751614-0.0218498573470.502694802644-28.450777052-1.1750069194238.6901266614
61.2964952507-1.45585770774-0.2878527452596.35544081576-0.3451608919620.606060820842-0.08198259923750.0383454057282-0.1674352022570.1541643480420.02955223517340.203561370382-0.156653383821-0.05738818669380.0446239994360.546595400464-0.01364981946780.08197111005260.32562487646-0.04571821344550.369571062017-13.9596140483-28.068660643128.8512923894
74.144053558212.40937036778-1.352310582396.08635335161-1.728770460711.518676402690.0619793135711-0.3024921079190.06140411098240.298495921683-0.003604836183930.350852884803-0.073048633925-0.239503664423-0.03775198231840.5807201465870.02737891984510.06479388348480.3972446870420.04276750168980.374779346974-23.037696342-16.600453086435.4484373499
81.4064694826-0.2758353828110.2509809254511.98906745223-1.436018359370.93029141303-0.0751570042777-0.754263879682-0.6527516161930.271550128340.262406481269-0.015605458776-0.5021102349770.3747431389-0.1692304002080.885876464421-0.07741037269030.08367846729260.44654512045-0.07705554065150.653513610703-17.0778125877-21.903756285860.0694577486
95.50338139618-0.277073016596-1.450943645388.674866699723.131677687862.087279325430.2649670766990.03792045353840.140920524230.337691198446-0.04953557598640.318015038183-0.6247352554460.0747873956877-0.1955755383520.669319205728-0.0104790090455-0.03710103069850.4334960357520.07753868587270.355432687866-9.79706295452-21.686701294253.9783605237
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 48 )AA0 - 481 - 49
22chain 'A' and (resid 49 through 269 )AA49 - 26950 - 270
33chain 'A' and (resid 270 through 373 )AA270 - 373271 - 374
44chain 'A' and (resid 374 through 455 )AA374 - 455375 - 456
55chain 'B' and (resid 1 through 48 )BC1 - 481 - 48
66chain 'B' and (resid 49 through 200 )BC49 - 20049 - 200
77chain 'B' and (resid 201 through 344 )BC201 - 344201 - 344
88chain 'B' and (resid 345 through 373 )BC345 - 373345 - 373
99chain 'B' and (resid 374 through 455 )BC374 - 455374 - 455

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