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- PDB-1xgf: Backbone Structure of COCOSIN, an 11S storage protein from cocos ... -

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Basic information

Entry
Database: PDB / ID: 1xgf
TitleBackbone Structure of COCOSIN, an 11S storage protein from cocos nucifera
Componentscocosin
KeywordsGlobulin / STORAGE PROTEIN / COCONUT ENDOSPERM / HEXAMER
Biological speciesCocos nucifera (coconut palm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsBalasundaresan, D. / Ponnuswamy, M.N.
Citation
Journal: TO BE PUBLISHED
Title: CRYSTAL STRUCTURE OF COCOSIN FROM COCOS NUCIFERA, A BACKBONE MODEL
Authors: Balasundaresan, D. / Ponnuswamy, M.N.
#1: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 2002
Title: Purification and crystallization of coconut globulin cocosin from cocos nucifera
Authors: Balasundaresan, D. / Sugadev, R. / Ponnuswamy, M.N.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal structure of soybean 11S globulin: Glycinin A3B4 homohexamer
Authors: ADACHI, M. / KANAMORI, J. / MASUDA, T. / YAGASAKI, K. / KITAMURA, K. / MIKAMI, B. / UTSUMI, S.
History
DepositionSep 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 21, 2016Group: Other
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Aug 23, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 400COMPOUND THESE ARE SEED STORAGE PROTEINS THAT EXIST AS HEXAMERIC ASSEMBLIES. EACH SUBUNIT IS ...COMPOUND THESE ARE SEED STORAGE PROTEINS THAT EXIST AS HEXAMERIC ASSEMBLIES. EACH SUBUNIT IS COMPOSED OF AN ACIDIC AND A BASIC CHAIN DERIVED FROM A SINGLE PRECURSOR THAT IS LINKED BY A DISULFIDE BOND. MEMBER OF THE 11S FAMILY OF GLOBULINS
Remark 999SEQUENCE SINCE NO SEQUENCE INFORMATION IS AVAILABLE,THE RESIDUES HAVE BEEN CHANGED TO UNK AND ONLY ...SEQUENCE SINCE NO SEQUENCE INFORMATION IS AVAILABLE,THE RESIDUES HAVE BEEN CHANGED TO UNK AND ONLY THE BACKBONE COORDINATES ARE GIVEN. THERE ARE FOUR DISORDERED REGIONS IN EACH CHAIN, NAMELY THE RESIDUES FROM 1 TO 6,93 TO 107, 179 TO 199 AND 252 TO 320.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cocosin
B: cocosin


Theoretical massNumber of molelcules
Total (without water)65,0562
Polymers65,0562
Non-polymers00
Water00
1
A: cocosin
B: cocosin

A: cocosin
B: cocosin

A: cocosin
B: cocosin


Theoretical massNumber of molelcules
Total (without water)195,1686
Polymers195,1686
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)93.659, 93.659, 216.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a hexamer generated from the molecule in the asymmetric unit by the operation: -Y,X-Y,Z, Y-X,-X,Z, X+2/3,Y+1/3,Z+1/3, -Y+2/3,X-Y+1/3,Z+1/3, Y-X+2/3,-X+1/3,Z+1/3, X+1/3,Y+2/3,Z+2/3, -Y+1/3,X-Y+2/3,Z+2/3, Y-X+1/3,-X+2/3,Z+2/3

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Components

#1: Protein cocosin


Mass: 32527.998 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cocos nucifera (coconut palm) / Tissue: endosperm

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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: 4.27 Å3/Da / Density % sol: 70.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 20% MPD, Na/K Phosphate buffer containing 7% NaCl, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 10, 2002
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 21429 / % possible obs: 99.8 % / Observed criterion σ(F): 1
Reflection shellResolution: 2.6→2.8 Å / Num. unique all: 21429 / % possible all: 93.78

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Processing

Software
NameClassification
MAR345data collection
AUTOMARdata reduction
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1OD5

1od5


Resolution: 2.61→2.8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: The coordinates contain backbone atoms only and are labelled as UNK since the sequence alignement is not established.There are several abnormal C-N bonds.
RfactorNum. reflectionSelection details
Rfree0.2944 1099 10%
Rwork0.2401 --
all0.2401 21429 -
obs0.2401 20330 -
Refinement stepCycle: LAST / Resolution: 2.61→2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 0 0 3056

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