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- PDB-1pva: COMPARISON BETWEEN THE CRYSTAL AND THE SOLUTION STRUCTURES OF THE... -

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Entry
Database: PDB / ID: 1pva
TitleCOMPARISON BETWEEN THE CRYSTAL AND THE SOLUTION STRUCTURES OF THE EF HAND PARVALBUMIN (ALPHA COMPONENT FROM PIKE MUSCLE)
ComponentsPARVALBUMIN
KeywordsCALCIUM BINDING
Function / homology
Function and homology information


ion binding / 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
Biological speciesEsox lucius (northern pike)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsDeclercq, J.P. / Tinant, B. / Roquet, F. / Rambaud, J. / Parello, J.
Citation
Journal: To be Published
Title: Comparison between the Crystal and the Solution Structures of the EF Hand Parvalbumin (Alpha Component from Pike Muscle)
Authors: Roquet, F. / Rambaud, J. / Declercq, J.P. / Tinant, B. / Baldellon, C. / Padilla, A. / Cave, A. / Parello, J.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Two-Dimensional 1H Nuclear Magnetic Resonance Study of Pike Pi 5.0 Parvalbumin (Esox Lucius): Sequential Resonance Assignments and Folding of the Polypeptide Chain
Authors: Padilla, A. / Cave, A. / Parello, J.
#3: 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
DepositionJan 16, 1995Processing site: BNL
Revision 1.0Mar 31, 1995Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PARVALBUMIN
B: PARVALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8096
Polymers23,6492
Non-polymers1604
Water3,099172
1
A: PARVALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9053
Polymers11,8241
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PARVALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9053
Polymers11,8241
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.700, 45.070, 81.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: THE ELECTRON DENSITY CORRESPONDING TO THE FIRST 6 RESIDUES (RESIDUES ACE B 0 - LEU B 5) OF MOLECULE B IS POORLY DEFINED.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9804, -0.008, 0.1969), (-0.0032, 0.9997, 0.0246), (-0.197, 0.0235, -0.9801)
Vector: 70.008, -1.853, 128.774)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 1 .. A 109 B 1 .. B 109 .696

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Components

#1: Protein PARVALBUMIN


Mass: 11824.427 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Esox lucius (northern pike) / References: UniProt: P02628
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.25 Å3/Da / Density % sol: 45.31 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 25503 / % possible obs: 97 % / Observed criterion σ(I): 0

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.65→8 Å / σ(F): 4
Details: THE ELECTRON DENSITY CORRESPONDING TO THE FIRST 6 RESIDUES (RESIDUES ACE B 0 - LEU B 5) OF MOLECULE B IS POORLY DEFINED.
RfactorNum. reflection% reflection
Rwork0.196 --
obs0.196 22984 88 %
Displacement parametersBiso mean: 18.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1668 0 4 172 1844
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.06
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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