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- PDB-2eaa: Crystal Structure of Adzuki Bean 7S Globulin-3 -

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Basic information

Entry
Database: PDB / ID: 2eaa
TitleCrystal Structure of Adzuki Bean 7S Globulin-3
Components7S globulin-3
KeywordsPLANT PROTEIN / BETA BARREL / CUPIN SUPERFAMILY
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
ACETIC ACID / CITRIC ACID / 7S globulin-3
Similarity search - Component
Biological speciesVigna angularis (adzuki bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsFukuda, T. / Mikami, B. / Utsumi, S.
CitationJournal: J.Agric.Food Chem. / Year: 2008
Title: Characterization and crystallography of recombinant 7S globulins of Adzuki bean and structure-function relationships with 7S globulins of various crops.
Authors: Fukuda, T. / Maruyama, N. / Salleh, M.R. / Mikami, B. / Utsumi, S.
History
DepositionJan 31, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 7S globulin-3
B: 7S globulin-3
C: 7S globulin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,34712
Polymers149,4713
Non-polymers8779
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16950 Å2
ΔGint-127 kcal/mol
Surface area40720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)66.873, 99.320, 216.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 7S globulin-3


Mass: 49823.512 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vigna angularis (adzuki bean) / Gene: 7S-3 / Plasmid: pEAdzuki7S3 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: A4PIA0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% MPD, 0.2M ammonium acetate, 0.1M Sodium citrate, 2.0M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 4, 2006 / Details: mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 69062 / Num. obs: 69062 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 19
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.415 / Num. unique all: 6784 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EA7

2ea7


Resolution: 2.25→15 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2656502.27 / 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
Rfree0.237 6954 10.1 %RANDOM
Rwork0.194 ---
obs0.194 68683 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.4143 Å2 / ksol: 0.351261 e/Å3
Displacement parametersBiso mean: 39.5 Å2
Baniso -1Baniso -2Baniso -3
1-14.02 Å20 Å20 Å2
2---6.85 Å20 Å2
3----7.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.25→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9148 0 54 481 9683
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.252.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 1093 10 %
Rwork0.265 9815 -
obs--95.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4acy.param
X-RAY DIFFRACTION5cit.param

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