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- PDB-8k1w: Crystal structure of PLA2 from Saccharothrix espanaensis -

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Basic information

Entry
Database: PDB / ID: 8k1w
TitleCrystal structure of PLA2 from Saccharothrix espanaensis
ComponentsPLA2
KeywordsHYDROLASE
Function / homologyPhospholipase A2, prokaryotic/fungal / Prokaryotic phospholipase A2 / phospholipase A2 activity / Phospholipase A2 domain superfamily / arachidonate secretion / phospholipid metabolic process / Putative secreted protein
Function and homology information
Biological speciesSaccharothrix espanaensis DSM 44229 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.30193016757 Å
AuthorsZhang, Z.M. / Wang, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of PLA2 from Saccharothrix espanaensis
Authors: Zhang, Z.M.
History
DepositionJul 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLA2


Theoretical massNumber of molelcules
Total (without water)14,4721
Polymers14,4721
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6450 Å2
Unit cell
Length a, b, c (Å)32.741, 37.679, 84.557
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein PLA2


Mass: 14471.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharothrix espanaensis DSM 44229 (bacteria)
Strain: DSM 44229 / Gene: BN6_69480 / Production host: Escherichia coli (E. coli) / References: UniProt: K0KBJ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.8 Å3/Da / Density % sol: 31.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M Tris-HCl, pH 8.5, 30% 2-Propanol, 30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 26771 / % possible obs: 100 % / Redundancy: 11.9 % / CC1/2: 0.994 / Net I/σ(I): 25
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 1276 / CC1/2: 0.962

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
autoPROCdata processing
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.30193016757→34.4166685094 Å / SU ML: 0.0759910977461 / Cross valid method: FREE R-VALUE / σ(F): 1.38421975396 / Phase error: 15.2823014113
RfactorNum. reflection% reflection
Rfree0.156880547326 2031 7.58656755444 %
Rwork0.152539211299 24740 -
obs0.152838555594 26771 54.0926633125 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.4191999352 Å2
Refinement stepCycle: LAST / Resolution: 1.30193016757→34.4166685094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms970 0 0 150 1120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005976954798751003
X-RAY DIFFRACTIONf_angle_d1.067994146251355
X-RAY DIFFRACTIONf_chiral_restr0.0385791292718129
X-RAY DIFFRACTIONf_plane_restr0.00651298279597181
X-RAY DIFFRACTIONf_dihedral_angle_d13.8777491715352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.30194-1.33220.1900614017941220.1723885787881467X-RAY DIFFRACTION48.4156002438
1.3322-1.36550.1596246292311250.1535539845181547X-RAY DIFFRACTION50.3462812406
1.3655-1.40250.1853016284011300.1638847060911561X-RAY DIFFRACTION51.3046116505
1.4025-1.44370.1924071481651280.1528436407891558X-RAY DIFFRACTION51.2617816966
1.4437-1.49030.1611918836741300.1473571862231588X-RAY DIFFRACTION52.092177077
1.4903-1.54360.1601409510921310.1391173529311588X-RAY DIFFRACTION52.2651261782
1.5436-1.60540.1737332300781310.1408078211751600X-RAY DIFFRACTION52.5022747953
1.6054-1.67850.1729541624271330.1407175026341606X-RAY DIFFRACTION52.7609223301
1.6785-1.76690.1729447915481320.1484682196221627X-RAY DIFFRACTION53.3515316955
1.7669-1.87760.1638812872781400.1534442789431692X-RAY DIFFRACTION55.0480769231
1.8776-2.02260.1443116607431410.158477638381705X-RAY DIFFRACTION55.9224477431
2.0226-2.22610.1779780583151450.1387726781981720X-RAY DIFFRACTION56.5837378641
2.2261-2.54810.1555118815061450.1597751187451788X-RAY DIFFRACTION58.6824529447
2.5481-3.210.163916271471470.1595035954051798X-RAY DIFFRACTION59.0646826602
3.21-34.410.1306354091941510.1524987329931895X-RAY DIFFRACTION61.8500604595
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)
14.10615498788-0.246270603186-0.3405943753273.953424249982.058555829145.23946717106-0.03891405265680.127904468785-0.0655085105004-0.200472742004-0.00315149729472-0.1543902791770.06547847891850.1218296577850.1391989444210.1428641686960.005657027555780.01565557644750.124848246351-0.01859938962120.15469907530716.7801094612-8.94525282828-16.6969422624
22.827134124481.47312729804-0.3937278297244.11727235501-1.338239599523.356806533270.0266192887236-0.00387280316614-0.1884155465070.02870364824290.0633624834718-0.1245442756840.06650854502290.1075359578-0.001261191912330.1131218062720.00657296235330.001350595459980.150998747816-0.004756783949730.12235670858121.3700624508-1.19540605161-9.0304772299
30.5554813332350.15934224628-0.1309753730810.4338514298630.3404227928031.348192811620.006064409332620.04009200972880.0409779474929-0.0358036041064-0.0182637724990.0105743555668-0.0424482162713-0.09563305394780.02069684879170.1159352240590.003403195195120.001079244822290.1213650752480.001998880410230.11583310299910.58793324261.72423688649-11.1931485883
41.419338400560.4407761406730.8136453023360.8576710749930.5314764314751.40063206314-0.0453166046578-0.0604726276213-0.02844827003550.03197235058870.03545804909130.03068295209160.030685964515-0.03054923591640.009946787470980.1260105454960.001720936500330.01363420980340.1197173067980.01167722521610.1201574665495.77576580423-2.166621466830.587062944367
50.4087373805740.4973557654120.0723606474111.130208692120.1083610813251.453885560740.380829110517-0.485843482336-1.01443404060.6204160704610.165620770743-0.9948601225411.021110342580.899716382022-0.517040628330.331552262023-0.0347493248089-0.1418722714350.4123071546830.06685016372280.38393817537-2.218064994895.10006826746-12.5248305165
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 28 )
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 114 )
5X-RAY DIFFRACTION5chain 'A' and (resid 115 through 121 )

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