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- PDB-1rtp: REFINED X-RAY STRUCTURE OF RAT PARVALBUMIN, A MAMMALIAN ALPHA-LIN... -

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Basic information

Entry
Database: PDB / ID: 1rtp
TitleREFINED X-RAY STRUCTURE OF RAT PARVALBUMIN, A MAMMALIAN ALPHA-LINEAGE PARVALBUMIN, AT 2.0 A RESOLUTION
ComponentsALPHA-PARVALBUMIN
KeywordsCALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


inhibitory chemical synaptic transmission / cuticular plate / excitatory chemical synaptic transmission / stereocilium / cochlea development / terminal bouton / gene expression / axon / neuronal cell body / calcium ion binding ...inhibitory chemical synaptic transmission / cuticular plate / excitatory chemical synaptic transmission / stereocilium / cochlea development / terminal bouton / gene expression / axon / neuronal cell body / calcium ion binding / protein-containing complex binding / protein-containing complex / identical protein 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
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsMcphalen, C.A. / Sielecki, A.R. / Santarsiero, B.D. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: Refined crystal structure of rat parvalbumin, a mammalian alpha-lineage parvalbumin, at 2.0 A resolution.
Authors: McPhalen, C.A. / Sielecki, A.R. / Santarsiero, B.D. / James, M.N.
History
DepositionMay 14, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: 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 / 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.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
1: ALPHA-PARVALBUMIN
2: ALPHA-PARVALBUMIN
3: ALPHA-PARVALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6809
Polymers35,4403
Non-polymers2406
Water1,982110
1
1: ALPHA-PARVALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8933
Polymers11,8131
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
2: ALPHA-PARVALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8933
Polymers11,8131
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
3: ALPHA-PARVALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8933
Polymers11,8131
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.300, 55.000, 156.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ALPHA-PARVALBUMIN


Mass: 11813.341 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / References: UniProt: P02625
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal grow
*PLUS
pH: 4.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19 mg/mlprotein1drop
280 %satammonium sulfate1reservoir
350 mM1reservoirNaOAc
41 %PEG6001reservoir
512 mM1reservoirCaCl2

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 23813 / Num. measured all: 96999 / Rmerge(I) obs: 0.059

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.181 20252
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 6 110 2600
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.01
X-RAY DIFFRACTIONp_angle_d0.030.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0260.02
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.72
X-RAY DIFFRACTIONp_mcangle_it2.22
X-RAY DIFFRACTIONp_scbond_it3.83
X-RAY DIFFRACTIONp_scangle_it5.33
X-RAY DIFFRACTIONp_plane_restr0.0080.01
X-RAY DIFFRACTIONp_chiral_restr0.1530.1
X-RAY DIFFRACTIONp_singtor_nbd0.2690.4
X-RAY DIFFRACTIONp_multtor_nbd0.2020.4
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2180.4
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.52.5
X-RAY DIFFRACTIONp_staggered_tor20.4100
X-RAY DIFFRACTIONp_orthonormal_tor24.6100
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. reflection all: 20869 / Num. reflection obs: 20252 / σ(F): 2 / Rfactor all: 0.203 / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_mcbond_it1.71
X-RAY DIFFRACTIONp_scbond_it3.87
X-RAY DIFFRACTIONp_mcangle_it2.25
X-RAY DIFFRACTIONp_scangle_it5.32

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