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- PDB-3kgl: Crystal structure of procruciferin, 11S globulin from Brassica napus -

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Basic information

Entry
Database: PDB / ID: 3kgl
TitleCrystal structure of procruciferin, 11S globulin from Brassica napus
ComponentsCruciferin
KeywordsPLANT PROTEIN / procruciferin / 11S seed globulin / Brassica napus / rapeseed / 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 / Jelly Rolls ...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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBrassica napus (rape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.981 Å
AuthorsTandang-Silvas, M.R. / 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
DepositionOct 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cruciferin
B: Cruciferin
C: Cruciferin
D: Cruciferin
E: Cruciferin
F: Cruciferin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,17416
Polymers308,2376
Non-polymers93710
Water3,351186
1
A: Cruciferin
B: Cruciferin
C: Cruciferin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,5878
Polymers154,1193
Non-polymers4685
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16840 Å2
ΔGint-64 kcal/mol
Surface area40200 Å2
MethodPISA
2
D: Cruciferin
E: Cruciferin
F: Cruciferin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,5878
Polymers154,1193
Non-polymers4685
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16910 Å2
ΔGint-59 kcal/mol
Surface area40410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.102, 190.412, 99.901
Angle α, β, γ (deg.)90.00, 114.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cruciferin


Mass: 51372.910 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica napus (rape) / Gene: Plant Gene / Plasmid: pET21-d, pETcru2/3a / Production host: Escherichia coli (E. coli) / Strain (production host): AD494(DE3) / References: UniProt: Q7XB53
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 32% ammonium sulfate, 0.1M MES pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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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 29, 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: 2.981→50 Å / Num. all: 68497 / Num. obs: 65757 / % possible obs: 96 % / Observed criterion σ(I): 3 / Redundancy: 6.1 % / Biso Wilson estimate: 55.546 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 14.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.81 / Num. unique all: 6644 / % possible all: 96.8

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Processing

Software
NameVersionClassification
JUPITER210data collection
CNSrefinement
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FXZ

1fxz


Resolution: 2.981→49.787 Å / SU ML: 0.4 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 3296 5.02 %RANDOM
Rwork0.1576 ---
obs0.1624 65651 94.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.693 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso mean: 49.44 Å2
Baniso -1Baniso -2Baniso -3
1--6.6021 Å20 Å24.3143 Å2
2--12.3614 Å20 Å2
3----5.7593 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.981→49.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18463 0 56 186 18705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918910
X-RAY DIFFRACTIONf_angle_d1.23325659
X-RAY DIFFRACTIONf_dihedral_angle_d20.3246947
X-RAY DIFFRACTIONf_chiral_restr0.082829
X-RAY DIFFRACTIONf_plane_restr0.0063427
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9814-3.0240.3254900.2261170161
3.024-3.06910.28061310.2022265698
3.0691-3.1170.3071600.1929265296
3.117-3.16810.37941240.1893267397
3.1681-3.22280.31151360.174263395
3.2228-3.28140.2781300.1517265198
3.2814-3.34450.30631390.1596264196
3.3445-3.41270.28811300.1822266497
3.4127-3.48690.29061510.1646261296
3.4869-3.5680.26581290.1557264995
3.568-3.65720.27421450.1426260797
3.6572-3.7560.22271390.1395263796
3.756-3.86650.231300.1334263395
3.8665-3.99130.2651570.1325261795
3.9913-4.13390.23711130.1246264296
4.1339-4.29930.22571510.1165259695
4.2993-4.49480.17181440.1173259795
4.4948-4.73160.19761500.1183259494
4.7316-5.02780.21011340.1202259394
5.0278-5.41560.21051350.1277259594
5.4156-5.95980.23631370.1473258293
5.9598-6.82030.26981420.1601260194
6.8203-8.58570.19241450.1436273199
8.5857-49.79350.21691540.1772798100

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