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- PDB-1b8l: Calcium-bound D51A/E101D/F102W Triple Mutant of Beta Carp Parvalbumin -

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Basic information

Entry
Database: PDB / ID: 1b8l
TitleCalcium-bound D51A/E101D/F102W Triple Mutant of Beta Carp Parvalbumin
ComponentsPROTEIN (PARVALBUMIN)
KeywordsCALCIUM BINDING PROTEIN / EF-HAND PROTEINS / PARVALBUMIN / CALCIUM-BINDING
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
CARBONATE ION / Parvalbumin beta
Similarity search - Component
Biological speciesCyprinus carpio (common carp)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCates, M.S. / Berry, M.B. / Ho, E. / Li, Q. / Potter, J.D. / Phillips Jr., G.N.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: Metal-ion affinity and specificity in EF-hand proteins: coordination geometry and domain plasticity in parvalbumin.
Authors: Cates, M.S. / Berry, M.B. / Ho, E.L. / Li, Q. / Potter, J.D. / Phillips Jr., G.N.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: Restrained Least Squares Refinement of Native (Calcium) and Cadmium- Substituted Carp Parvalbumin Using X-Ray Crystallographic Data at 1.6 Angstrom Resolution
Authors: Swain, A.L. / Kretsinger, R.H. / Amma, E.L.
History
DepositionFeb 1, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 5, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_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: PROTEIN (PARVALBUMIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5323
Polymers11,4321
Non-polymers1002
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.511, 37.298, 37.067
Angle α, β, γ (deg.)90.00, 113.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (PARVALBUMIN)


Mass: 11431.790 Da / Num. of mol.: 1 / Mutation: D51A, E101D, F102W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyprinus carpio (common carp) / Production host: Escherichia coli (E. coli) / References: UniProt: P02618
#2: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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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: 1.51 Å3/Da / Density % sol: 35.91 %
Description: ALTERNATE CONFORMATION MODELED FOR SIDE CHAIN LYS 3
Crystal growpH: 6.9
Details: CRYSTALLIZATION CONDITIONS 40% PEG 4000, 50 MM CACL2, 50 M PH 7.0, 4 DEGREES C, pH 6.9
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMHEPES1reservoir
250 mM1reservoirCaCl2
340 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 3, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 9239 / % possible obs: 84.2 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.038
Reflection
*PLUS
% possible obs: 94 % / Rmerge(I) obs: 0.065

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Processing

Software
NameClassification
SHELXL-97refinement
SHELXmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CPV, AUTH A.L.SWAIN,R.H.KRETSINGER, E.L.AMMA

5cpv


Resolution: 1.7→40 Å / Num. parameters: 3903 / Num. restraintsaints: 3327 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 950 11.7 %RANDOM
all0.1672 8141 --
obs0.1678 -84.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 794 / Occupancy sum non hydrogen: 970
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms811 0 5 159 975
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.015
X-RAY DIFFRACTIONs_similar_dist0.001
X-RAY DIFFRACTIONs_from_restr_planes0.0229
X-RAY DIFFRACTIONs_zero_chiral_vol0.043
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.043
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.024
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 11.7 % / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.015

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