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- PDB-1a75: WHITING PARVALBUMIN -

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Basic information

Entry
Database: PDB / ID: 1a75
TitleWHITING PARVALBUMIN
Components(PARVALBUMIN) x 2
KeywordsCALCIUM BINDING PROTEIN / MUSCLE PROTEIN
Function / homology
Function and homology information


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 speciesMerlangius merlangus (whiting)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDeclercq, J.P. / Baneres, J.L. / Rambaud, J. / Parello, J.
Citation
Journal: To be Published
Title: Tertiary Structure of a Trp-Containing Parvalbumin from Whiting (Merlangius Merlangus). Description of the Hydrophobic Core
Authors: Declercq, J.P. / Baneres, J.L. / Rambaud, J. / Parello, J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: X-Ray Structure of a New Crystal Form of Pike 4.10 Beta Parvalbumin
Authors: Declercq, J.P. / Tinant, B. / Parello, J.
#2: 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.
#3: 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.
#4: 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
DepositionMar 19, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
B: PARVALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8586
Polymers22,6982
Non-polymers1604
Water4,234235
1
A: PARVALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4163
Polymers11,3361
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PARVALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4423
Polymers11,3621
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.730, 27.590, 98.510
Angle α, β, γ (deg.)90.00, 91.49, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9998, -0.0184, 0.0012), (-0.0183, -0.9966, -0.0801), (0.0027, 0.0801, -0.9968)
Vector: 18.792, 37.602, 146.166)

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Components

#1: Protein PARVALBUMIN


Mass: 11335.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Merlangius merlangus (whiting) / Tissue: MUSCLE / References: UniProt: P02621
#2: Protein PARVALBUMIN


Mass: 11361.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Merlangius merlangus (whiting) / Tissue: MUSCLE / References: UniProt: P02621
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 235 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 41 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: SITTING DROP. RESERVOIR: 1 ML 2.1M NAH2PO4/NA2HPO4 (PH 6.0) 0.7M (NH4)2SO4, 0.02%(W/V) NAN3 DROP: 10 MICROL. PROTEIN SOLUTION (15MG/ML) +10 MICROL. RESERVOIR SOLUTION., vapor diffusion - sitting drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→12 Å / Num. obs: 12412 / % possible obs: 82.2 % / Redundancy: 1.54 % / Rsym value: 0.057 / Net I/σ(I): 8.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 1.48 % / Mean I/σ(I) obs: 5 / Rsym value: 0.12 / % possible all: 73.2

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5CPV

5cpv


Resolution: 1.9→12 Å / Num. parameters: 7243 / Num. restraintsaints: 7757 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
all0.2139 12412 -
obs0.2139 -82.2 %
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1810
Refinement stepCycle: LAST / Resolution: 1.9→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1568 0 7 235 1810
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.017
X-RAY DIFFRACTIONs_similar_dist0.039
X-RAY DIFFRACTIONs_from_restr_planes0.311
X-RAY DIFFRACTIONs_zero_chiral_vol0.024
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.034
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.061
X-RAY DIFFRACTIONs_approx_iso_adps0

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