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- PDB-1pal: IONIC INTERACTIONS WITH PARVALBUMINS. CRYSTAL STRUCTURE DETERMINA... -

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Basic information

Entry
Database: PDB / ID: 1pal
TitleIONIC INTERACTIONS WITH PARVALBUMINS. CRYSTAL STRUCTURE DETERMINATION OF PIKE 4.10 PARVALBUMIN IN FOUR DIFFERENT IONIC ENVIRONMENTS
ComponentsPARVALBUMIN
KeywordsCALCIUM BINDING PROTEIN
Function / homology
Function and homology information


axon terminus / axon / dendrite / calcium ion binding / cytoplasm
Similarity search - Function
Parvalbumin / 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 ...Parvalbumin / 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
AMMONIUM ION / Parvalbumin beta
Similarity search - Component
Biological speciesEsox lucius (northern pike)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsDeclercq, J.P. / Tinant, B. / Parello, J. / Rambaud, J.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Ionic interactions with parvalbumins. Crystal structure determination of pike 4.10 parvalbumin in four different ionic environments.
Authors: Declercq, J.P. / Tinant, B. / Parello, J. / Rambaud, J.
#1: 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, R.
History
DepositionNov 8, 1990Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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.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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PARVALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5284
Polymers11,4301
Non-polymers983
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.500, 59.630, 26.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-224-

HOH

21A-257-

HOH

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Components

#1: Protein PARVALBUMIN


Mass: 11429.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Esox lucius (northern pike) / References: UniProt: P02619
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 3 mM / Common name: sodium azide

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 9999 Å / Num. obs: 11782 / % possible obs: 74 % / Observed criterion σ(I): 1 / Num. measured all: 29643 / Rmerge(I) obs: 0.101
Reflection shell
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 1.8 Å / % possible obs: 53 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.197 / Highest resolution: 1.65 Å
Refinement stepCycle: LAST / Highest resolution: 1.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms805 0 3 64 872
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0240.03
X-RAY DIFFRACTIONp_angle_d0.0640.06
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0960.08
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it5.67
X-RAY DIFFRACTIONp_mcangle_it6.58
X-RAY DIFFRACTIONp_scbond_it910
X-RAY DIFFRACTIONp_scangle_it10.812
X-RAY DIFFRACTIONp_plane_restr0.0170.025
X-RAY DIFFRACTIONp_chiral_restr0.370.3
X-RAY DIFFRACTIONp_singtor_nbd0.20.5
X-RAY DIFFRACTIONp_multtor_nbd0.220.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.20.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.84
X-RAY DIFFRACTIONp_staggered_tor2420
X-RAY DIFFRACTIONp_orthonormal_tor2420
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 1.8 Å / Rfactor obs: 0.255

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