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- PDB-3ksc: Crystal structure of pea prolegumin, an 11S seed globulin from Pi... -

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Basic information

Entry
Database: PDB / ID: 3ksc
TitleCrystal structure of pea prolegumin, an 11S seed globulin from Pisum sativum L.
ComponentsLegA class
KeywordsPLANT PROTEIN / pea prolegumin / 11S seed storage protein / Pisum sativum L. / Seed storage protein / Storage protein
Function / homology
Function and homology information


nutrient reservoir activity
Similarity search - Function
11-S seed storage protein, conserved site / 11-S plant seed storage proteins signature. / 11-S seed storage protein, plant / : / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold ...11-S seed storage protein, conserved site / 11-S plant seed storage proteins signature. / 11-S seed storage protein, plant / : / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Legumin A / LegA class
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.606 Å
AuthorsTandang-Silvas, M.R.G. / Fukuda, T. / Fukuda, C. / Prak, K. / Cabanos, C. / Kimura, A. / Itoh, T. / Mikami, B. / Maruyama, N. / Utsumi, S.
CitationJournal: Biochim.Biophys.Acta / Year: 2010
Title: Conservation and divergence on plant seed 11S globulins based on crystal structures.
Authors: Tandang-Silvas, M.R. / Fukuda, T. / Fukuda, C. / Prak, K. / Cabanos, C. / Kimura, A. / Itoh, T. / Mikami, B. / Utsumi, S. / Maruyama, N.
History
DepositionNov 21, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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: LegA class
B: LegA class
C: LegA class
D: LegA class
E: LegA class
F: LegA class
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,91737
Polymers340,0116
Non-polymers2,90731
Water6,143341
1
A: LegA class
B: LegA class
C: LegA class
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,97924
Polymers170,0053
Non-polymers1,97421
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16050 Å2
ΔGint-84 kcal/mol
Surface area38890 Å2
MethodPISA
2
D: LegA class
E: LegA class
F: LegA class
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,93813
Polymers170,0053
Non-polymers93310
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16230 Å2
ΔGint-81 kcal/mol
Surface area39370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.777, 148.441, 149.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 8:88 or resseq 107:175 or resseq 187:235 or resseq 318:487 )
211chain B and (resseq 8:88 or resseq 107:175 or resseq 187:235 or resseq 318:487 )
311chain C and (resseq 8:88 or resseq 107:175 or resseq 187:235 or resseq 318:487 )
411chain D and (resseq 8:88 or resseq 107:175 or resseq 187:235 or resseq 318:487 )
511chain E and (resseq 8:88 or resseq 107:175 or resseq 187:235 or resseq 318:487 )
611chain F and (resseq 8:88 or resseq 107:175 or resseq...

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Components

#1: Protein
LegA class / prolegumin


Mass: 56668.484 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: legA, Plant gene / Plasmid: pET21-d, pEpea11S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9T0P5, UniProt: P02857*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.0M ammonium sulfate, 0.2M K/Na tartrate, 0.1M sodium citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 24, 2007 / Details: Graphite monochromator
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 88747 / Num. obs: 88303 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 5.6 % / Biso Wilson estimate: 39.64 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.18 / Num. unique all: 8624 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FXZ

1fxz


Resolution: 2.606→49.057 Å / SU ML: 0.32 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 4426 5.02 %random
Rwork0.1752 ---
obs0.1781 88213 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.993 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso mean: 36.94 Å2
Baniso -1Baniso -2Baniso -3
1--6.6013 Å20 Å20 Å2
2---0.6401 Å20 Å2
3---7.2414 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.606→49.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18033 0 173 341 18547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618553
X-RAY DIFFRACTIONf_angle_d0.98625063
X-RAY DIFFRACTIONf_dihedral_angle_d20.4256866
X-RAY DIFFRACTIONf_chiral_restr0.0682695
X-RAY DIFFRACTIONf_plane_restr0.0043348
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2922X-RAY DIFFRACTIONPOSITIONAL
12B2922X-RAY DIFFRACTIONPOSITIONAL0.757
13C2922X-RAY DIFFRACTIONPOSITIONAL0.813
14D2922X-RAY DIFFRACTIONPOSITIONAL0.809
15E2922X-RAY DIFFRACTIONPOSITIONAL0.714
16F2939X-RAY DIFFRACTIONPOSITIONAL0.712
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6062-2.63580.33151460.247248590
2.6358-2.66680.31661370.2309270898
2.6668-2.69930.29531390.2154280799
2.6993-2.73350.30931320.2093273499
2.7335-2.76950.26831560.2067275899
2.7695-2.80740.28751590.1982273499
2.8074-2.84750.29121410.1971278599
2.8475-2.890.27641330.1952278599
2.89-2.93520.2731620.1918275799
2.9352-2.98330.26681450.1942757100
2.9833-3.03470.27321470.19532783100
3.0347-3.08990.27391260.1891281799
3.0899-3.14930.2711470.18982781100
3.1493-3.21360.25111480.18472763100
3.2136-3.28340.2711460.1703277899
3.2834-3.35980.23031500.15842795100
3.3598-3.44380.20081560.1559278199
3.4438-3.53690.25691220.15992823100
3.5369-3.64090.20731400.15832814100
3.6409-3.75840.21911660.1562789100
3.7584-3.89270.2181680.15242774100
3.8927-4.04850.19261520.15042824100
4.0485-4.23260.20251350.14772823100
4.2326-4.45560.19071290.13952837100
4.4556-4.73460.17751390.14042846100
4.7346-5.09980.19541480.15332852100
5.0998-5.61230.22691620.16372839100
5.6123-6.42290.23691550.182880100
6.4229-8.08630.21711770.16822869100
8.0863-49.06540.19391630.1964300999

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