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- PDB-4iau: Atomic resolution structure of Geodin, a beta-gamma crystallin fr... -

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Basic information

Entry
Database: PDB / ID: 4iau
TitleAtomic resolution structure of Geodin, a beta-gamma crystallin from Geodia cydonium
ComponentsBeta-gamma-crystallin
KeywordsUNKNOWN FUNCTION / Greek key strand motif
Function / homology
Function and homology information


Crystallins / Gamma-B Crystallin; domain 1 / Beta/Gamma crystallin / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta-gamma-crystallin
Similarity search - Component
Biological speciesGeodia cydonium (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.99 Å
AuthorsVergara, A. / Grassi, M. / Sica, F. / Mazzarella, L. / Merlino, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: A novel interdomain interface in crystallins: structural characterization of the [beta][gamma]-crystallin from Geodia cydonium at 0.99 A resolution
Authors: Vergara, A. / Grassi, M. / Sica, F. / Pizzo, E. / D'Alessio, G. / Mazzarella, L. / Merlino, A.
History
DepositionDec 7, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: Beta-gamma-crystallin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5266
Polymers18,1181
Non-polymers4085
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.170, 61.302, 50.175
Angle α, β, γ (deg.)90.00, 95.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-gamma-crystallin


Mass: 18117.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geodia cydonium (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: O18426
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.04 Å3/Da / Density % sol: 39.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M ammonium sulphate, 17 % w/v PEG 8000, 2mM dithiotreitol, 50mM Tris-HCl (pH 7.6) , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 3, 2008 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.99→20 Å / Num. all: 80711 / Num. obs: 80711 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.064

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
SHELXLrefinement
RefinementMethod to determine structure: SAD / Resolution: 0.99→20 Å / Occupancy max: 1 / Occupancy min: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.129 4017 random
Rwork0.106 --
all0.107 80505 -
obs0.106 80505 -
Displacement parametersBiso max: 157.89 Å2 / Biso mean: 14.2752 Å2 / Biso min: 1.96 Å2
Refinement stepCycle: LAST / Resolution: 0.99→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 25 370 1639

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