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- PDB-3qac: Structure of amaranth 11S proglobulin seed storage protein from A... -

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Basic information

Entry
Database: PDB / ID: 3qac
TitleStructure of amaranth 11S proglobulin seed storage protein from Amaranthus hypochondriacus L.
Components11S globulin seed storage protein
KeywordsPLANT PROTEIN / 11S seed storage protein (globulins) family / seed 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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
11S globulin seed storage protein
Similarity search - Component
Biological speciesAmaranthus hypochondriacus (grain amaranth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.275 Å
AuthorsTandang-Silvas, M.R. / Carrazco-Pena, L. / Barba de la Rosa, A.P. / Osuna-Castro, J.A. / Utsumi, S. / Mikami, B. / Maruyama, N.
Citation
Journal: To be Published
Title: Structure of amaranth 11S proglobulin, a major seed storage protein from Amaranthus hypochondriacus L.
Authors: Tandang-Silvas, M.R. / Carrazco-Pena, L. / Barba de la Rosa, A.P. / Osuna-Castro, J.A. / Utsumi, S. / Mikami, B. / Maruyama, N.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Expression, purification and preliminary crystallization of amaranth 11S proglobulin seed storage protein from Amaranthus hypochondriacus L.
Authors: Tandang-Silvas, M.R. / Carrazco-Pena, L. / Barba de la Rosa, A.P. / Osuna-Castro, J.A. / Utsumi, S. / Mikami, B. / Maruyama, N.
History
DepositionJan 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 11S globulin seed storage protein


Theoretical massNumber of molelcules
Total (without water)52,7221
Polymers52,7221
Non-polymers00
Water1,802100
1
A: 11S globulin seed storage protein

A: 11S globulin seed storage protein

A: 11S globulin seed storage protein


Theoretical massNumber of molelcules
Total (without water)158,1663
Polymers158,1663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area15210 Å2
ΔGint-62 kcal/mol
Surface area37300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.077, 94.077, 74.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

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Components

#1: Protein 11S globulin seed storage protein


Mass: 52721.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amaranthus hypochondriacus (grain amaranth)
Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami(DE3) / References: UniProt: Q38712
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 1.81 Å3/Da / Density % sol: 32.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 16% PEG3350, 200mM ammonium formate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 5, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.275→50 Å / Num. all: 17239 / Num. obs: 17067 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 4.01 / Num. unique all: 860 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E9Q

2e9q


Resolution: 2.275→28.468 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7811 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 864 5.07 %RANDOM
Rwork0.1875 ---
obs0.1906 17027 98.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.331 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 97.18 Å2 / Biso mean: 49.2937 Å2 / Biso min: 25.93 Å2
Baniso -1Baniso -2Baniso -3
1-6.5351 Å2-0 Å2-0 Å2
2--6.5351 Å2-0 Å2
3----13.0702 Å2
Refinement stepCycle: LAST / Resolution: 2.275→28.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2927 0 0 100 3027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092984
X-RAY DIFFRACTIONf_angle_d1.2164035
X-RAY DIFFRACTIONf_chiral_restr0.074443
X-RAY DIFFRACTIONf_plane_restr0.004540
X-RAY DIFFRACTIONf_dihedral_angle_d20.4341096
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2753-2.41780.31371310.24682588271994
2.4178-2.60430.33781440.24762710285499
2.6043-2.86620.35181500.22832701285199
2.8662-3.28040.25821480.19782687283598
3.2804-4.1310.20211540.15642719287399
4.131-28.47030.21751370.16992758289598

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