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- PDB-2pvb: PIKE PARVALBUMIN (PI 4.10) AT LOW TEMPERATURE (100K) AND ATOMIC R... -

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Basic information

Entry
Database: PDB / ID: 2pvb
TitlePIKE PARVALBUMIN (PI 4.10) AT LOW TEMPERATURE (100K) AND ATOMIC RESOLUTION (0.91 A).
ComponentsPROTEIN (PARVALBUMIN)
KeywordsMETAL BINDING PROTEIN / CALCIUM BINDING PROTEIN
Function / homology
Function and homology information


axon terminus / axon / dendrite / 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
FORMIC ACID / AMMONIUM ION / Parvalbumin beta
Similarity search - Component
Biological speciesEsox lucius (northern pike)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 0.91 Å
AuthorsDeclercq, J.P. / Evrard, C.
Citation
Journal: Protein Sci. / Year: 1999
Title: Crystal structure of the EF-hand parvalbumin at atomic resolution (0.91 A) and at low temperature (100 K). Evidence for conformational multistates within the hydrophobic core.
Authors: Declercq, J.P. / Evrard, C. / Lamzin, V. / Parello, J.
#1: Journal: J.Cryst.Growth / Year: 1999
Title: A Crystal of a Typical EF-Hand Protein Grown Under Microgravity Diffracts X- Rays Beyond 0.9 A Resolution
Authors: Declercq, J.P. / Evrard, C. / Carter, D.C. / Wright, B.S. / Etienne, G. / Parello, J.
#2: 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.
#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
DepositionOct 2, 1998Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / diffrn_source / pdbx_initial_refinement_model / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)11,6206
Polymers11,4301
Non-polymers1905
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.030, 49.810, 34.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (PARVALBUMIN)


Mass: 11429.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: (PIKE PI 4.10) / Source: (natural) Esox lucius (northern pike) / Tissue: MUSCLE / References: UniProt: P02619
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsACETYL IS COVALENTLY ATTACHED TO THE N-TERMINAL SERINE BY AN AMIDE LINKAGE

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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: 1.93 Å3/Da / Density % sol: 36.2 % / Description: STRUCTURE PREVIOUSLY SOLVED AT 1.75 A
Crystal growMethod: vapor diffusion - sitting drop in microgravity / pH: 8
Details: SITTING DROP, MICROGRAVITY CONDITIONS PROTEIN SOLUTION : 27 MG/ML, 0.02% (W/V) NAN3 RESERVOIR : 2.4M AMMONIUM SULFATE 0.03%(W/V) EDTA, 0.02% (W/V) NAN3 TRIS BUFFER (PH 8.0) DROP : 10 MICROL. ...Details: SITTING DROP, MICROGRAVITY CONDITIONS PROTEIN SOLUTION : 27 MG/ML, 0.02% (W/V) NAN3 RESERVOIR : 2.4M AMMONIUM SULFATE 0.03%(W/V) EDTA, 0.02% (W/V) NAN3 TRIS BUFFER (PH 8.0) DROP : 10 MICROL. PROTEIN SOLUTION + 10 MICROL. RESERVOIR, vapor diffusion - sitting drop in microgravity
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Details: under microgravity, Declercq, J.P., (1999) J.Cryst.Growth, 196, 595.
PH range low: 8.25 / PH range high: 7.75
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.02 %sodium azide1drop
225-35 mg/mlprotein1drop
32.25-2.40 Mammonium sulfate1reservoir
40.3 mg/mlEDTA1reservoir
5Tris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9096
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: SEGMENTED MIRROR
RadiationMonochromator: BENT SINGLE-CRYSTAL GERMANIUM TRIANGULAR MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9096 Å / Relative weight: 1
ReflectionResolution: 0.91→25 Å / Num. obs: 63698 / % possible obs: 99.8 % / Redundancy: 4.9 % / Rsym value: 3.6 / Net I/σ(I): 14.2
Reflection shellResolution: 0.91→0.92 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.3 / Rsym value: 12.4 / % possible all: 97.3
Reflection
*PLUS
Num. measured all: 481972 / Rmerge(I) obs: 0.036

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1PVB

1pvb


Resolution: 0.91→25 Å / Num. parameters: 9883 / Num. restraintsaints: 12405 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1317 3187 5 %RANDOM, 5%
all0.1098 63698 --
obs0.1095 -99.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 16 / Occupancy sum hydrogen: 784 / Occupancy sum non hydrogen: 1025
Refinement stepCycle: LAST / Resolution: 0.91→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms873 0 6 217 1096
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.335
X-RAY DIFFRACTIONs_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.102
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.061
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.037
X-RAY DIFFRACTIONs_approx_iso_adps0.1
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor all: 0.11 / Rfactor Rfree: 0.132 / Rfactor Rwork: 0.109
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_chiral_restr0.10.102
LS refinement shell
*PLUS
Highest resolution: 0.91 Å / Lowest resolution: 0.94 Å / Rfactor all: 0.132

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