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- PDB-1xvj: Crystal Structure Of Rat alpha-Parvalbumin D94S/G98E Mutant -

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Basic information

Entry
Database: PDB / ID: 1xvj
TitleCrystal Structure Of Rat alpha-Parvalbumin D94S/G98E Mutant
ComponentsParvalbumin alpha
KeywordsMETAL BINDING PROTEIN / parvalbumin / calcium-binding protein / EF hand 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 norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTanner, J.J. / Agah, S. / Lee, Y.H. / Henzl, M.T.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal Structure of the D94S/G98E Variant of Rat alpha-Parvalbumin. An Explanation for the Reduced Divalent Ion Affinity.
Authors: Tanner, J.J. / Agah, S. / Lee, Y.H. / Henzl, M.T.
History
DepositionOct 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Parvalbumin alpha
B: Parvalbumin alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8756
Polymers23,7152
Non-polymers1604
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.719, 56.988, 56.493
Angle α, β, γ (deg.)90.00, 105.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Parvalbumin alpha


Mass: 11857.393 Da / Num. of mol.: 2 / Mutation: D94S, G98E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pvalb, Pva / Production host: Escherichia coli (E. coli) / References: UniProt: P02625
#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.: 199 / 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: 1.984 Å3/Da / Density % sol: 38 %

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 25, 2003
RadiationMonochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→24.54 Å / Num. all: 15257 / Num. obs: 15257 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 25
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 9.6 / Rsym value: 0.224 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→24.54 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.116 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23582 780 4.9 %RANDOM
Rwork0.19693 ---
all0.19882 15257 --
obs0.19882 15257 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.697 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.02 Å2
2---0.28 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1653 0 4 199 1856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221671
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9782224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2125216
X-RAY DIFFRACTIONr_chiral_restr0.0890.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021198
X-RAY DIFFRACTIONr_nbd_refined0.1990.2817
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2140
X-RAY DIFFRACTIONr_metal_ion_refined0.0830.215
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.222
X-RAY DIFFRACTIONr_mcbond_it0.5311.51074
X-RAY DIFFRACTIONr_mcangle_it1.01121702
X-RAY DIFFRACTIONr_scbond_it1.8343597
X-RAY DIFFRACTIONr_scangle_it2.9844.5522
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.348 53
Rwork0.261 1041

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