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- PDB-1ht9: DOMAIN SWAPPING EF-HANDS -

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Basic information

Entry
Database: PDB / ID: 1ht9
TitleDOMAIN SWAPPING EF-HANDS
ComponentsCALBINDIN D9K
KeywordsMETAL BINDING PROTEIN / DOMAIN SWAPPING / CALBINDIN D9K / EF-HAND / CALCIUM BINDING / FOLDING
Function / homology
Function and homology information


vitamin D binding / calcium-dependent protein binding / collagen-containing extracellular matrix / calcium ion binding / extracellular space / cytoplasm
Similarity search - Function
S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / EF-hand / Recoverin; domain 1 / 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 / SIRAS, MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsHakansson, M. / Svensson, A.L. / Fast, J. / Linse, S.
Citation
Journal: Protein Sci. / Year: 2001
Title: An extended hydrophobic core induces EF-hand swapping.
Authors: Hakansson, M. / Svensson, A. / Fast, J. / Linse, S.
#1: Journal: To be Published
Title: Symmetric Stabilization of Bound Ca2+ Ions Through Hydrogen Bonding of Coordinating Water Molecules. Ca2+ Binding Abd Structural Stability of Calbindin D9K Mutants
Authors: Fast, J. / Muranyi, A. / Gippert, G.P. / Thulin, E. / Evenas, J. / Linse, S. / Hakansson, M. / Svensson, A.L.
History
DepositionDec 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 21, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: pdbx_struct_conn_angle / refine ...pdbx_struct_conn_angle / refine / reflns_shell / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_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 / _refine.ls_percent_reflns_obs / _reflns_shell.percent_possible_all / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALBINDIN D9K
B: CALBINDIN D9K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4846
Polymers17,3242
Non-polymers1604
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-86 kcal/mol
Surface area8820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.605, 48.241, 41.530
Angle α, β, γ (deg.)90.00, 96.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CALBINDIN D9K


Mass: 8661.807 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PICB1 / Production host: Escherichia coli (E. coli) / Strain (production host): MM294 / References: UniProt: P02633
#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 / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1.87 Å3/Da / Density % sol: 34.25 %
Crystal growTemperature: 293 K / Method: evaporation
Details: ammonium sulphate, calcium chloride, magnesium chloride, EVAPORATION, temperature 293K
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
135-40 mg/mlprotein1drop
21.3-2.2 mM1dropCaCl2
360-70 %ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 9, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→44 Å / Num. obs: 50352 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.5
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 3.7 / % possible all: 60
Reflection
*PLUS
Lowest resolution: 44 Å / Num. obs: 11923 / Num. measured all: 50352
Reflection shell
*PLUS
% possible obs: 60.1 %

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Processing

Software
NameClassification
MLPHAREphasing
AMoREphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SIRAS, MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ICB

4icb


Resolution: 1.76→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.192 588 -RANDOM
Rwork0.162 ---
obs-11907 93 %-
Displacement parametersBiso mean: 23.9 Å2
Refinement stepCycle: LAST / Resolution: 1.76→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 4 86 1306
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d0.027
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg22.7

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