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- PDB-2e9q: Recombinant pro-11S globulin of pumpkin -

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Basic information

Entry
Database: PDB / ID: 2e9q
TitleRecombinant pro-11S globulin of pumpkin
Components11S globulin subunit beta
KeywordsPLANT PROTEIN / CUCUBITIN / PUMPKIN SEED STORAGE GLOBULIN
Function / homology
Function and homology information


nutrient reservoir activity / metal ion binding
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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / 11S globulin subunit beta
Similarity search - Component
Biological speciesCucurbita maxima (winter squash)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsFukuda, T. / Prak, K. / Itoh, T. / Masuda, T. / Maruyama, N. / Mikami, B. / 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
DepositionJan 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 11S globulin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5233
Polymers52,3931
Non-polymers1302
Water1,856103
1
A: 11S globulin subunit beta
hetero molecules

A: 11S globulin subunit beta
hetero molecules

A: 11S globulin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,5699
Polymers157,1783
Non-polymers3916
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_545z,x-1/2,y+1/21
crystal symmetry operation45_545y+1/2,z-1/2,x1
Buried area17220 Å2
ΔGint-137 kcal/mol
Surface area41050 Å2
MethodPISA
2
A: 11S globulin subunit beta
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)630,27636
Polymers628,71112
Non-polymers1,56524
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation17_545z,x-1/2,y+1/21
crystal symmetry operation18_544z,-x-1/2,-y-1/21
crystal symmetry operation19_545-z,-x-1/2,y+1/21
crystal symmetry operation20_544-z,x-1/2,-y-1/21
crystal symmetry operation45_545y+1/2,z-1/2,x1
crystal symmetry operation46_445-y-1/2,z-1/2,-x1
crystal symmetry operation47_545y+1/2,-z-1/2,-x1
crystal symmetry operation48_445-y-1/2,-z-1/2,x1
Buried area83980 Å2
ΔGint-566 kcal/mol
Surface area149070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)188.997, 188.997, 188.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23

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Components

#1: Protein 11S globulin subunit beta / pro-11S GLOBULIN CUCURBITIN


Mass: 52392.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cucurbita maxima (winter squash) / Plasmid: pET21d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13744
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE DEPOSITORS BELIEVE THAT GLY46 AND GLU294 ARE CORRECT AND THAT SWISSPROT IS INCORRECT AT THESE POSITIONS.

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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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M NaCl, 0.1M Na/K phosphate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Dec 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 28317 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 122
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 2EVX

2evx


Resolution: 2.2→14.94 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 6082737.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 2815 9.9 %RANDOM
Rwork0.223 ---
obs0.223 28317 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.369 Å2 / ksol: 0.334128 e/Å3
Displacement parametersBiso mean: 58.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3070 0 6 103 3179
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it4.991.5
X-RAY DIFFRACTIONc_mcangle_it6.242
X-RAY DIFFRACTIONc_scbond_it6.612
X-RAY DIFFRACTIONc_scangle_it8.552.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.402 449 9.5 %
Rwork0.305 4264 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4po4_xplor_parampo4_xplor_top

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