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- PDB-2cv6: Crystal Structure of 8Salpha Globulin, the Major Seed Storage Pro... -

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Basic information

Entry
Database: PDB / ID: 2cv6
TitleCrystal Structure of 8Salpha Globulin, the Major Seed Storage Protein of Mungbean
ComponentsSeed storage protein
KeywordsPLANT PROTEIN / cupin
Function / homology
Function and homology information


: / 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
8S globulin alpha isoform
Similarity search - Component
Biological speciesVigna radiata (mung bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsItoh, T. / Garcia, R.N. / Adachi, M. / Maruyama, Y. / Tecson-Mendoza, E.M. / Mikami, B. / Utsumi, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of 8Salpha globulin, the major seed storage protein of mung bean.
Authors: Itoh, T. / Garcia, R.N. / Adachi, M. / Maruyama, Y. / Tecson-Mendoza, E.M. / Mikami, B. / Utsumi, S.
History
DepositionMay 31, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Seed storage protein


Theoretical massNumber of molelcules
Total (without water)48,7311
Polymers48,7311
Non-polymers00
Water1448
1
A: Seed storage protein

A: Seed storage protein

A: Seed storage protein


Theoretical massNumber of molelcules
Total (without water)146,1943
Polymers146,1943
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area15690 Å2
ΔGint-107 kcal/mol
Surface area39790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)146.600, 146.600, 53.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a trimer.

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Components

#1: Protein Seed storage protein


Mass: 48731.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vigna radiata (mung bean) / Plasmid: PET21d / Production host: Escherichia coli (E. coli) / References: UniProt: Q198W5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.3 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 1000, NaCl, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.54 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.61→37 Å / Num. all: 33649 / Num. obs: 11640 / % possible obs: 89.6 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 38.7 Å2
Reflection shellResolution: 2.61→2.71 Å / % possible all: 71

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Processing

Software
NameVersionClassification
CNS1.1refinement
SADIEdata reduction
SAINTdata reduction
SAINTdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→9.99 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 531730.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: CRYST1 TEXT TO EXPLAIN UNUSUAL UNIT-CELL DATA: HEXAGONAL OBVERSE SETTING
RfactorNum. reflection% reflectionSelection details
Rfree0.258 560 5.2 %RANDOM
Rwork0.196 ---
obs0.196 10853 89.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.2037 Å2 / ksol: 0.331602 e/Å3
Displacement parametersBiso mean: 52.4 Å2
Baniso -1Baniso -2Baniso -3
1--16.89 Å2-0.25 Å20 Å2
2---16.89 Å20 Å2
3---33.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.65→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2976 0 0 8 2984
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.192
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.992.5
LS refinement shellResolution: 2.65→2.81 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.43 79 5.4 %
Rwork0.356 1379 -
obs--71.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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