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- PDB-1bjf: CRYSTAL STRUCTURE OF RECOMBINANT BOVINE NEUROCALCIN DELTA AT 2.4 ... -

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Basic information

Entry
Database: PDB / ID: 1bjf
TitleCRYSTAL STRUCTURE OF RECOMBINANT BOVINE NEUROCALCIN DELTA AT 2.4 ANGSTROMS
ComponentsNEUROCALCIN DELTA
KeywordsCALCIUM-BINDING / MYRISTOYLATION / NEURONAL SPECIFIC GUANYLATE CYCLASE ACTIVATOR
Function / homology
Function and homology information


Activation of Ca-permeable Kainate Receptor / regulation of systemic arterial blood pressure / clathrin binding / tubulin binding / calcium-mediated signaling / actin binding / calcium ion binding
Similarity search - Function
Recoverin family / EF-hand domain pair / 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 ...Recoverin family / EF-hand domain pair / 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 speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.4 Å
AuthorsVijay-Kumar, S. / Kumar, V.D.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Crystal structure of recombinant bovine neurocalcin.
Authors: Vijay-Kumar, S. / Kumar, V.D.
History
DepositionJun 25, 1998Processing site: BNL
Revision 1.0Jul 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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.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_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_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: NEUROCALCIN DELTA
B: NEUROCALCIN DELTA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7898
Polymers44,5492
Non-polymers2406
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-85 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.680, 93.350, 50.625
Angle α, β, γ (deg.)90.00, 98.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.473089, -0.846549, 0.244009), (-0.851305, -0.510571, -0.120816), (0.226861, -0.150569, -0.962218)
Vector: 11.27731, 21.92868, 9.56027)

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Components

#1: Protein NEUROCALCIN DELTA


Mass: 22274.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Strain: DH5-ALPHA / Cellular location: CYTOPLASM / Plasmid: PMAL-C / Production host: Escherichia coli (E. coli) / References: UniProt: P61602
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 20

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 45 %
Crystal growpH: 6.1 / Details: pH 6.1
Crystal grow
*PLUS
Temperature: 20-25 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
245-50 %satammonium sulfate1reservoir
350 mMPIPES1reservoir
45 mM1reservoirCaCl2
50.5 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 1, 1997
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.4 Å / Num. obs: 12105 / % possible obs: 84.3 % / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073
Reflection shellResolution: 2.4→2.49 Å / % possible all: 54.2
Reflection shell
*PLUS
% possible obs: 54.2 %

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Processing

Software
NameVersionClassification
X-PLOR3.84model building
X-PLOR3.84refinement
R-AXISdata reduction
R-AXISdata scaling
X-PLOR3.84phasing
RefinementMethod to determine structure: MIR / Resolution: 2.4→40 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1345 10.4 %RANDOM
Rwork0.218 ---
obs0.218 12990 84.3 %-
Displacement parametersBiso mean: 35.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2991 0 7 44 3042
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.27
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.051.5
X-RAY DIFFRACTIONx_mcangle_it4.442
X-RAY DIFFRACTIONx_scbond_it4.742
X-RAY DIFFRACTIONx_scangle_it6.932.5
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 130 10.5 %
Rwork0.378 1111 -
obs--48.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.84 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.27

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