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- PDB-2wg8: Structure of Oryza Sativa (Rice) PLA2, orthorhombic crystal form -

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Basic information

Entry
Database: PDB / ID: 2wg8
TitleStructure of Oryza Sativa (Rice) PLA2, orthorhombic crystal form
Components(PUTATIVE PHOSPHOLIPASE A2) x 2
KeywordsHYDROLASE / SECRETORY PLA2
Function / homology
Function and homology information


phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / lipid binding / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Probable phospholipase A2 homolog 2
Similarity search - Component
Biological speciesORYZA SATIVA (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGuy, J.E. / Stahl, U. / Lindqvist, Y.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal Structure of a Class Xib Phospholipase A2 (Pla2): Rice (Oryza Sativa) Isoform-2 Pla2 and an Octanoate Complex.
Authors: Guy, J.E. / Stahl, U. / Lindqvist, Y.
History
DepositionApr 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE PHOSPHOLIPASE A2
B: PUTATIVE PHOSPHOLIPASE A2
C: PUTATIVE PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9297
Polymers41,7863
Non-polymers1434
Water3,711206
1
A: PUTATIVE PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9782
Polymers13,9381
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PUTATIVE PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9873
Polymers13,9241
Non-polymers632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PUTATIVE PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9642
Polymers13,9241
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)169.094, 41.491, 53.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A15 - 119
2115B15 - 119
1126A17 - 119
2126C17 - 119

NCS ensembles :
ID
1
2

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Components

#1: Protein PUTATIVE PHOSPHOLIPASE A2 / / PLA2


Mass: 13937.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ORYZA SATIVA (Asian cultivated rice) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER DE3 / References: UniProt: Q9XG81, phospholipase A2
#2: Protein PUTATIVE PHOSPHOLIPASE A2 / / PLA2


Mass: 13923.841 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ORYZA SATIVA (Asian cultivated rice) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER DE3 / References: UniProt: Q9XG81, phospholipase A2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCESSION NUMBER PROVIDED BY AUTHOR IS NCBI REFERENCE NP_001049620.1. THE DEPOSITED SEQUENCE ...ACCESSION NUMBER PROVIDED BY AUTHOR IS NCBI REFERENCE NP_001049620.1. THE DEPOSITED SEQUENCE INCLUDES THE SIGNAL SEQUENCE, OUR CONSTRUCT DOES NOT.

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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: 2.48 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: VAPOUR DIFFUSION, 20 DEGREES. WELL CONTAINED 0.75ML OF SOLN A (16-18% PEG3350, 0.1M BISTRISPROPANE PH 6.5, 0.2M POTASSIUM THIOCYANATE) AND 0.25ML OF SOLN B (0.1M SODIUM ACETATE PH 4.6, 2M SODIUM CHLORIDE)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 15584 / % possible obs: 94.7 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 17.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 5.4 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P62 CRYSTAL FORM

Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.891 / SU B: 11.555 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24505 846 5.1 %RANDOM
Rwork0.1898 ---
obs0.19271 15584 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.486 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 4 206 2669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212538
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9583456
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9735335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.58124.352108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20915405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6661515
X-RAY DIFFRACTIONr_chiral_restr0.070.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021914
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.21235
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.21782
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2154
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1310.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3941.51644
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.75522640
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2963906
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0924.5812
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A412medium positional0.20.5
12B412medium positional0.20.5
11A358loose positional0.465
12B358loose positional0.465
21A770loose positional0.455
22C770loose positional0.455
11A412medium thermal0.492
12B412medium thermal0.492
11A358loose thermal1.1610
12B358loose thermal1.1610
21A770loose thermal210
22C770loose thermal210
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 55 -
Rwork0.206 1091 -
obs--93.78 %
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)
13.8205-0.3899-0.70242.7515-0.97332.59120.05230.08970.1061-0.1084-0.0183-0.06510.02830.2546-0.0341-0.15480.0031-0.0075-0.15150.0006-0.0843-16.86636.3797-20.3666
22.6507-0.5105-0.91744.09681.02691.97210.02750.41770.1407-0.3755-0.021-0.1916-0.08650.0463-0.0064-0.09010.0130.0108-0.11060.0647-0.0701-25.475125.5468-25.4951
32.68070.41640.35241.2594-0.35694.99660.0233-0.02760.19-0.00510.1018-0.27360.11970.5642-0.1251-0.1209-0.0070.0312-0.1345-0.0467-0.0288-32.799241.777-47.8242
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 122
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION2B2 - 7
4X-RAY DIFFRACTION2B14 - 121
5X-RAY DIFFRACTION2B201
6X-RAY DIFFRACTION3C15 - 121

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