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- PDB-2bv2: beta gamma crystallin from Ciona Intestinalis -

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Basic information

Entry
Database: PDB / ID: 2bv2
Titlebeta gamma crystallin from Ciona Intestinalis
ComponentsCIONA BETAGAMMA-CRYSTALLIN
KeywordsCRYSTALLIN / CALCIUM BINDING / EYE LENS / SPHERULIN / CHORDATE / ASCIDIAN
Function / homologyCrystallins / Gamma-B Crystallin; domain 1 / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesCIONA INTESTINALIS (vase tunicate)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsShimeld, S.M. / Purkiss, A.G. / Dirks, R.P.H. / Bateman, O.A. / Slingsby, C. / Lubsen, N.H.
CitationJournal: Curr.Biol. / Year: 2005
Title: Urochordate Betagamma-Crystallin and the Evolutionary Origin of the Vertebrate Eye Lens.
Authors: Shimeld, S.M. / Purkiss, A.G. / Dirks, R.P.H. / Bateman, O.A. / Slingsby, C. / Lubsen, N.H.
History
DepositionJun 21, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CIONA BETAGAMMA-CRYSTALLIN
B: CIONA BETAGAMMA-CRYSTALLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4438
Polymers18,1282
Non-polymers3156
Water2,180121
1
A: CIONA BETAGAMMA-CRYSTALLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2995
Polymers9,0641
Non-polymers2354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CIONA BETAGAMMA-CRYSTALLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1443
Polymers9,0641
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.037, 29.788, 57.278
Angle α, β, γ (deg.)90.00, 121.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-262-

HOH

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Components

#1: Protein CIONA BETAGAMMA-CRYSTALLIN


Mass: 9063.897 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CIONA INTESTINALIS (vase tunicate) / Cell: PALPS, OTOLITH / Production host: ESCHERICHIA COLI (E. coli)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE ENTRY FOR THIS PROTEIN IS NOT CURRENTLY AVAILABLE IN UNIPROT. THE GB REFERENCE ...A SEQUENCE DATABASE ENTRY FOR THIS PROTEIN IS NOT CURRENTLY AVAILABLE IN UNIPROT. THE GB REFERENCE FOR THIS PROTEIN IS 23575069

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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 Å3/Da / Density % sol: 37 %
Description: TWO DATASETS COLLECTED, A HIGH RESOLUTION PASS AND A LOW RESOULTION PASS. MERGED WITH SCALA
Crystal growpH: 4.6
Details: 0.2M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE PH4.6, 30PERCENT PEGMME 2000, WITH ADDITION OF CALCIUM ACETATE, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 28, 2004 / Details: MIRROR
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 21220 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 2.6
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 1.8 / % possible all: 87.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1HA4, 1HK0, 1OKI, C-TERMINAL DOMAINS SUPERIMPOSED

1ha4

1hk0

1oki


Resolution: 1.55→17.01 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.279 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 987 5.1 %RANDOM
Rwork0.169 ---
obs0.173 18382 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.46 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.55→17.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1278 0 13 121 1412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221324
X-RAY DIFFRACTIONr_bond_other_d0.0010.021127
X-RAY DIFFRACTIONr_angle_refined_deg1.2391.9571794
X-RAY DIFFRACTIONr_angle_other_deg0.73932657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9125164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.17726.39361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85215212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02256
X-RAY DIFFRACTIONr_nbd_refined0.1930.2281
X-RAY DIFFRACTIONr_nbd_other0.1740.21162
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2666
X-RAY DIFFRACTIONr_nbtor_other0.0870.2721
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3170.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1450.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3732845
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.08331324
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7772560
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.3113470
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.302 66
Rwork0.151 1261

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