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- PDB-1b9a: PARVALBUMIN (MUTATION;D51A, F102W) -

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Basic information

Entry
Database: PDB / ID: 1b9a
TitlePARVALBUMIN (MUTATION;D51A, F102W)
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
Biological speciesCyprinus carpio (common carp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCates, M.S. / Berry, M.B. / Ho, E.L. / 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 10, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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_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.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

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Assembly

Deposited unit
A: PROTEIN (PARVALBUMIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5263
Polymers11,4461
Non-polymers802
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.424, 33.424, 298.186
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-163-

HOH

21A-180-

HOH

31A-181-

HOH

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Components

#1: Protein PROTEIN (PARVALBUMIN)


Mass: 11445.816 Da / Num. of mol.: 1 / Mutation: D51A, 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growpH: 7 / Details: pH 7.0
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: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.743318
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jun 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.743318 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 5432 / % possible obs: 73 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.069
Reflection
*PLUS
% possible obs: 73 %

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Processing

Software
NameVersionClassification
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CPV, AUTH A.L.SWAIN,R.H.KRETSINGER, E.L.AMMA

5cpv


Resolution: 2→40 Å / Rfactor Rfree error: 0.012 / Data cutoff high rms absF: 723489.75 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2902 576 10.6 %RANDOM
Rwork0.2096 ---
obs-5432 73 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.41 Å2 / ksol: 0.3181 e/Å3
Displacement parametersBiso mean: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å2-3 Å20 Å2
2--1.94 Å20 Å2
3----3.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms807 0 2 173 982
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.65
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.641.5
X-RAY DIFFRACTIONx_mcangle_it2.462
X-RAY DIFFRACTIONx_scbond_it2.072
X-RAY DIFFRACTIONx_scangle_it2.912.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.403 75 12.2 %
Rwork0.275 538 -
obs--50.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.2096
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.65
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.403 / % reflection Rfree: 12.2 % / Rfactor Rwork: 0.275

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