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Basic information

Entry
Database: PDB / ID: 7jiz
TitleScDLH
ComponentsDienelactone hydrolase family protein
KeywordsHYDROLASE / dienelactonase / phosphotriesterase
Function / homologyDienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold / hydrolase activity / Dienelactone hydrolase family protein
Function and homology information
Biological speciesSolimonas sp. K1W22B-7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSchnettler Fernandez, J.D.F. / Campbell, E.C. / Hollfelder, F.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Commission695669 United Kingdom
Citation
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJul 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: Dienelactone hydrolase family protein
B: Dienelactone hydrolase family protein


Theoretical massNumber of molelcules
Total (without water)54,0592
Polymers54,0592
Non-polymers00
Water9,170509
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-0 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.550, 123.604, 46.655
Angle α, β, γ (deg.)90.000, 100.979, 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 Dienelactone hydrolase family protein


Mass: 27029.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solimonas sp. K1W22B-7 (bacteria) / Gene: D0B54_07315 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A346MYW6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% w/v PEG3000, 0.1 M Tris, pH 7, 0.2 M calcium acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 3, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.85→42.75 Å / Num. obs: 40398 / % possible obs: 97.87 % / Redundancy: 6.7 % / Biso Wilson estimate: 23.73 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08356 / Net I/σ(I): 13.14
Reflection shellResolution: 1.85→1.916 Å / Rmerge(I) obs: 0.5364 / Mean I/σ(I) obs: 3.64 / Num. unique obs: 4112 / CC1/2: 0.909 / % possible all: 99.76

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F67

3f67


Resolution: 1.85→42.75 Å / SU ML: 0.1917 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2885
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.195 2040 5.05 %
Rwork0.1658 38332 -
obs0.1672 40372 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.09 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3596 0 0 509 4105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033784
X-RAY DIFFRACTIONf_angle_d0.57185156
X-RAY DIFFRACTIONf_chiral_restr0.0421550
X-RAY DIFFRACTIONf_plane_restr0.0042702
X-RAY DIFFRACTIONf_dihedral_angle_d23.43521358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.32251470.23782635X-RAY DIFFRACTION100
1.89-1.940.42911540.32752544X-RAY DIFFRACTION99.08
1.94-1.990.24331410.19432584X-RAY DIFFRACTION99.96
1.99-2.050.21451510.17842601X-RAY DIFFRACTION99.96
2.05-2.120.20331400.1782607X-RAY DIFFRACTION99.96
2.12-2.190.23041240.16972603X-RAY DIFFRACTION99.96
2.19-2.280.21031000.18061811X-RAY DIFFRACTION70
2.28-2.390.20831390.15822619X-RAY DIFFRACTION100
2.39-2.510.22091510.16842581X-RAY DIFFRACTION100
2.51-2.670.1911280.1682620X-RAY DIFFRACTION99.96
2.67-2.870.19751260.17012632X-RAY DIFFRACTION100
2.87-3.160.18571150.16652628X-RAY DIFFRACTION100
3.16-3.620.18081340.15372632X-RAY DIFFRACTION99.82
3.62-4.560.13941300.13862607X-RAY DIFFRACTION99.78
4.56-42.750.17371600.15332628X-RAY DIFFRACTION99.61
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)
14.4822802571-1.76741041935-1.05535870874.080972455320.08120224169854.09088060157-0.127041146454-0.450537834428-0.2878922186760.716041040631-0.02428620340260.410708903940.3331320132-0.04666779649710.1495969551260.257000554413-0.06395953630860.02557533991180.1861207385850.02535487955510.2287015707730.284-23.44429.235
22.07924711558-0.842349141860.2243065043352.46901200835-0.186679380982.933893805310.02081483547810.185945000754-0.102680587417-0.0721514442304-0.0918089272467-0.0707892153780.2264203811430.2893134174610.05742856554280.1718640915-0.0143920957277-0.002361482599550.197673773554-0.0005620021748230.1940819107276.036-24.29716.038
31.545500741390.594716955022-0.3971666248672.89551303381-1.917856486164.622783713370.1033175260660.00882028925305-0.06869784741920.1766017812320.01086830785860.232695183977-0.137031791407-0.384889462405-0.03272291525010.16643342325-0.0123508408069-0.01168300726910.164655001948-0.0273682641470.184161285927-2.584-18.9421.613
42.607313273390.7420639684270.2592702776283.614436939130.1657767328492.431645044980.1328733064320.274311821538-0.144120402566-0.184092949628-0.107864705226-0.1628191218760.04011878789940.0670801560323-0.006549779556850.1401458399080.0473335368761-0.005785834692110.13496440813-0.00519243939830.13178717324.801-9.78111.845
53.63881088147-1.162692619360.4150265416632.93017482550.02042486442982.89694068757-0.0281186999315-0.4182384681820.1651832788720.366092238645-0.00204451035371-0.0625156789475-0.2887489481360.185027032701-0.01173285097260.203919960303-0.02818048142760.02365641767740.212305894627-0.002562317304740.19547014627812.69722.85229.524
62.39231841062-1.226273154151.124310906744.26245140574-2.086643538576.00605321439-0.104758420137-0.147952877003-0.254544834160.3830870747970.06812901091780.7508208901860.0632504516641-0.972826146557-0.06012918170860.164433810074-0.01783662917170.04449627608640.246489020777-0.02545530820740.2723824946193.24519.62423.393
71.46901534911-0.6880852545320.1890349910161.15181822365-0.06087980557182.42305965614-0.02775864286020.01392786222250.114009780050.130958638324-0.05778080119350.08536624979290.00332399700585-0.04021865208890.02220861448950.136006199882-0.0283665313094-0.004252396509370.11148366836-0.001242320064110.16950826920710.28524.08121.924
81.16611397854-0.675381305587-0.4587966456091.509811519660.4394247647922.018927868610.1540286751120.2538021370010.291634373053-0.318333563474-0.1995674963850.0265852404146-0.229145642612-0.0817628333250.03716500203030.2563166607710.0107790004710.006984207921650.2032066119340.04360856497480.2390231767979.21627.5438.833
91.711290715211.012459037580.2351899425172.988473213771.968556888415.122533296360.0632088016019-0.0106516704604-0.04668583900170.1312077954940.0391177826034-0.1948161652520.06473054154240.421636117045-0.07046321892240.188613906070.02032911467980.01758269912630.16974218050.03414308103240.21169971462315.71318.71322.03
101.456637665910.801981681477-0.3490857540063.2691196057-0.273148559581.952029715540.005960332940550.196499560808-0.00345413968804-0.2948626450550.02340648956260.0114331950023-0.07737216635080.0266778518211-0.02265787689090.1611438037790.03907608741420.01910293376940.1484510112780.0406192932690.13033338374814.06612.5469.634
113.281723838920.349091523468-0.6760080820082.639837125990.1597792744092.183196949980.1980441295770.3379804364050.451207676706-0.278690559372-0.1088519004420.420616054504-0.287395662559-0.316226972403-0.06813513210690.2269646710190.0605759852318-0.008783424172460.1747901652930.05482777974710.2511153673424.3158.8539.137
124.319819223432.021390425832.339357433293.686345437721.455934888733.15665223760.213884878411-0.4908078361160.2284041422460.230844372126-0.2392154601150.4734204011330.150011182525-0.317916116350.03031916588160.213056201124-0.001189676228570.04847746862750.1919160379510.01477060583670.2459198409142.2525.82521.946
134.868826874231.748470517520.6871443286017.093190194871.456810923115.330847219430.136894656622-0.289910944936-0.2560931346540.50504086001-0.0899587587497-0.4491921535640.4317094190810.36879344692-0.1346005290960.2088054256270.03283604498047.02705367729E-50.1850906738460.02941166562990.13176295373216.5436.3625.423
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 13:34 )A13 - 34
2X-RAY DIFFRACTION2( CHAIN A AND RESID 35:100 )A35 - 100
3X-RAY DIFFRACTION3( CHAIN A AND RESID 101:125 )A101 - 125
4X-RAY DIFFRACTION4( CHAIN A AND RESID 126:238 )A126 - 238
5X-RAY DIFFRACTION5( CHAIN B AND RESID 13:34 )B13 - 34
6X-RAY DIFFRACTION6( CHAIN B AND RESID 35:55 )B35 - 55
7X-RAY DIFFRACTION7( CHAIN B AND RESID 56:67 )B56 - 67
8X-RAY DIFFRACTION8( CHAIN B AND RESID 68:100 )B68 - 100
9X-RAY DIFFRACTION9( CHAIN B AND RESID 101:125 )B101 - 125
10X-RAY DIFFRACTION10( CHAIN B AND RESID 126:171 )B126 - 171
11X-RAY DIFFRACTION11( CHAIN B AND RESID 172:218 )B172 - 218
12X-RAY DIFFRACTION12( CHAIN B AND RESID 219:231 )B219 - 231
13X-RAY DIFFRACTION13( CHAIN B AND RESID 232:238 )B232 - 238

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