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- PDB-5pal: CRYSTAL STRUCTURE OF THE UNIQUE PARVALBUMIN COMPONENT FROM MUSCLE... -

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Basic information

Entry
Database: PDB / ID: 5pal
TitleCRYSTAL STRUCTURE OF THE UNIQUE PARVALBUMIN COMPONENT FROM MUSCLE OF THE LEOPARD SHARK (TRIAKIS SEMIFASCIATA). THE FIRST X-RAY STUDY OF AN ALPHA-PARVALBUMIN
ComponentsPARVALBUMIN
KeywordsCALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
Parvalbumin / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain ...Parvalbumin / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / 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
Biological speciesTriakis semifasciata (leopard shark)
MethodX-RAY DIFFRACTION / Resolution: 1.54 Å
AuthorsRoquet, F. / Declercq, J.-P. / Tinant, B. / Rambaud, J. / Parello, J.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Crystal structure of the unique parvalbumin component from muscle of the leopard shark (Triakis semifasciata). The first X-ray study of an alpha-parvalbumin.
Authors: Roquet, F. / Declercq, J.P. / Tinant, B. / Rambaud, J. / Parello, J.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Ionic Interactions with Parvalbumins. Crystal Structure Determination of Pike 4(Dot)10 Parvalbumin in Four Different Ionic Environments
Authors: Declercq, J.-P. / Tinant, B. / Parello, J. / Rambaud, J.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Crystal Structure Determination and Refinement of Pike 4.10 Parvalbumin (Minor Component from Esox Lucius)
Authors: Declercq, J.-P. / Tinant, B. / Parello, J. / Etienne, G. / Huber, H.
History
DepositionSep 25, 1991Processing 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 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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: PARVALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0313
Polymers11,9501
Non-polymers802
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.120, 32.120, 149.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PARVALBUMIN /


Mass: 11950.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triakis semifasciata (leopard shark) / References: UniProt: P30563
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.74 %

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Processing

Software
NameClassification
X-PLORmodel building
EREFrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor obs: 0.173 / Highest resolution: 1.54 Å
Refinement stepCycle: LAST / Highest resolution: 1.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms841 0 2 92 935
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.011
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.33
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it

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