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- PDB-1rwy: CRYSTAL STRUCTURE OF RAT ALPHA-PARVALBUMIN AT 1.05 RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1rwy
TitleCRYSTAL STRUCTURE OF RAT ALPHA-PARVALBUMIN AT 1.05 RESOLUTION
ComponentsPARVALBUMIN ALPHA
KeywordsCALCIUM-BINDING PROTEIN / EF-HAND / CALCIUM-BINDING
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
ACETIC ACID / AMMONIUM ION / Parvalbumin alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsBottoms, C.A. / Schuermann, J.P. / Agah, S. / Henzl, M.T. / Tanner, J.J.
CitationJournal: Protein Sci. / Year: 2004
Title: Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution
Authors: Bottoms, C.A. / Schuermann, J.P. / Agah, S. / Henzl, M.T. / Tanner, J.J.
History
DepositionDec 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_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: PARVALBUMIN ALPHA
B: PARVALBUMIN ALPHA
C: PARVALBUMIN ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,33716
Polymers35,4403
Non-polymers89713
Water6,720373
1
A: PARVALBUMIN ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0505
Polymers11,8131
Non-polymers2364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PARVALBUMIN ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1826
Polymers11,8131
Non-polymers3685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PARVALBUMIN ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1065
Polymers11,8131
Non-polymers2924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.838, 54.708, 153.643
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein PARVALBUMIN ALPHA


Mass: 11813.341 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: FAST-TWITCH MUSCLE / Gene: PVALB, PVA / Plasmid: pBluescript / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P02625

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Non-polymers , 6 types, 386 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 1.69 Å3/Da / Density % sol: 27.1 %
Description: CNS WAS USED TO REFINE THE STARTING MODEL WITH A 1.55 DATA. SET WAS COLLECTED AT HOME. SHELX WAS USED TO REFINE THE RESULTING MODEL WITH THE 1.05 A DATASET COLLECTED AT APS-ID.
Crystal growTemperature: 298 K / pH: 4.6
Details: PEG, ammonium sulfate, sodium acetate, temperature 298K, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.94644
DetectorType: SBC-2 / Detector: CCD / Date: Jun 17, 2003 / Details: APS 19-ID
RadiationMonochromator: APS 19-ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94644 Å / Relative weight: 1
ReflectionResolution: 1.05→25.1 Å / Num. obs: 132869 / % possible obs: 99.2 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 36.2
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 4.6 / % possible all: 97.5

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Processing

Software
NameVersionClassification
SHELXL-97refinement
DENZOdata reduction
HKL-2000data reduction
SCALEPACKdata scaling
CNSrefinement
SHELXmodel building
HKL-2000data collection
HKL-2000(SCALEPACK)data scaling
CNSphasing
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RTP

1rtp


Resolution: 1.05→25.1 Å / Num. parameters: 26422 / Num. restraintsaints: 31383 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.024
RfactorNum. reflection% reflectionSelection details
Rfree0.162 6703 5.3 %RANDOM
all0.133 125945 --
obs0.133 125945 94.1 %-
Solvent computationSolvent model: SWAT (BABINET'S PRINCIPLE) (MOEWS & KRETSINGER).
Refine analyzeNum. disordered residues: 11 / Occupancy sum hydrogen: 2371 / Occupancy sum non hydrogen: 2867.5
Refinement stepCycle: LAST / Resolution: 1.05→25.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 40 377 2932
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0.017
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.076
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.034
X-RAY DIFFRACTIONs_approx_iso_adps0.064

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