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- PDB-2sas: STRUCTURE OF A SARCOPLASMIC CALCIUM-BINDING PROTEIN FROM AMPHIOXU... -

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Basic information

Entry
Database: PDB / ID: 2sas
TitleSTRUCTURE OF A SARCOPLASMIC CALCIUM-BINDING PROTEIN FROM AMPHIOXUS REFINED AT 2.4 ANGSTROMS RESOLUTION
ComponentsSARCOPLASMIC CALCIUM-BINDING PROTEIN
KeywordsCALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
EF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Sarcoplasmic calcium-binding proteins II, V, VI, and VII
Similarity search - Component
Biological speciesBranchiostoma lanceolatum (amphioxus)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsCook, W.J. / Babu, Y.S. / Cox, J.A.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Structure of a sarcoplasmic calcium-binding protein from amphioxus refined at 2.4 A resolution.
Authors: Cook, W.J. / Jeffrey, L.C. / Cox, J.A. / Vijay-Kumar, S.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization and Preliminary X-Ray Investigation of a Sarcoplasmic Calcium-Binding Protein from Amphioxus
Authors: Cook, W.J. / Babu, Y.S. / Cox, J.A.
History
DepositionJul 30, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Oct 23, 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_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_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.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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: SARCOPLASMIC CALCIUM-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4284
Polymers21,3081
Non-polymers1203
Water181
1
A: SARCOPLASMIC CALCIUM-BINDING PROTEIN
hetero molecules

A: SARCOPLASMIC CALCIUM-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8568
Polymers42,6162
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)59.600, 81.300, 82.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein SARCOPLASMIC CALCIUM-BINDING PROTEIN


Mass: 21307.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma lanceolatum (amphioxus) / References: UniProt: P04570
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal grow
*PLUS
Temperature: 24 ℃ / pH: 8.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein 1drop
22.5 mM1dropCaCl2
354 %satammonium sulfate1drop
40.05 MTris-HCl1drop
554 %satammonium sulfate1reservoir
60.05 MTris-HCl1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 8157 / % possible obs: 98.7 % / Num. measured all: 45101 / Rmerge(I) obs: 0.0909

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→5 Å / Rfactor Rwork: 0.199 / Rfactor obs: 0.199 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.4→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1495 0 3 1 1499
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.0881
X-RAY DIFFRACTIONx_mcangle_it1.6831.5
X-RAY DIFFRACTIONx_scbond_it1.8881.5
X-RAY DIFFRACTIONx_scangle_it2.6772
Software
*PLUS
Name: X-PLOR/PROLSQ / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.030.045
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_planar_d0.050.062
X-RAY DIFFRACTIONp_plane_restr0.020.014
X-RAY DIFFRACTIONp_chiral_restr0.150.153
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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