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- PDB-6fie: Crystallographic structure of calcium loaded Calbindin-D28K. -

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Basic information

Entry
Database: PDB / ID: 6fie
TitleCrystallographic structure of calcium loaded Calbindin-D28K.
ComponentsCalbindin
KeywordsMETAL BINDING PROTEIN / Calcium Binding Protein / Buffer / IMPase / EF-hand
Function / homology
Function and homology information


metanephric connecting tubule development / calcium ion binding involved in regulation of presynaptic cytosolic calcium ion concentration / calcium ion binding involved in regulation of postsynaptic cytosolic calcium ion concentration / metanephric distal convoluted tubule development / retina layer formation / metanephric part of ureteric bud development / cuticular plate / response to auditory stimulus / vitamin D binding / metanephric collecting duct development ...metanephric connecting tubule development / calcium ion binding involved in regulation of presynaptic cytosolic calcium ion concentration / calcium ion binding involved in regulation of postsynaptic cytosolic calcium ion concentration / metanephric distal convoluted tubule development / retina layer formation / metanephric part of ureteric bud development / cuticular plate / response to auditory stimulus / vitamin D binding / metanephric collecting duct development / short-term memory / stereocilium / cochlea development / postsynaptic cytosol / long-term memory / presynaptic cytosol / calyx of Held / hippocampal mossy fiber to CA3 synapse / regulation of synaptic plasticity / GABA-ergic synapse / terminal bouton / Amyloid fiber formation / axon / neuronal cell body / calcium ion binding / synapse / dendrite / glutamatergic synapse / extracellular exosome / zinc ion binding / nucleus / cytosol
Similarity search - Function
Calbindin / : / EF hand domain / 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. ...Calbindin / : / EF hand domain / 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
THIOCYANATE ION / Calbindin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsNoble, J.W. / Almalki, R. / Roe, S.M. / Wagner, A. / Dumanc, R. / Atack, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: The X-ray structure of human calbindin-D28K: an improved model.
Authors: Noble, J.W. / Almalki, R. / Roe, S.M. / Wagner, A. / Duman, R. / Atack, J.R.
History
DepositionJan 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Calbindin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5716
Polymers30,3521
Non-polymers2185
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-38 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.617, 104.222, 29.614
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Calbindin / Calbindin D28 / D-28K / Vitamin D-dependent calcium-binding protein / avian-type


Mass: 30352.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALB1, CAB27 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: P05937
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Sample: 41.6mg/ml Calbindin-D28k in 1mM CaCl 5mM Tris pH8.0 (HCl). Reservoir: 0.1M Potassium thiocyanate and 30% w/v PEG 2000 MME.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 14, 2017
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.51→29.61 Å / Num. obs: 41505 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 29.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.024 / Rrim(I) all: 0.048 / Net I/av σ(I): 14.4 / Net I/σ(I): 14.4
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2048 / CC1/2: 0.4 / Rpim(I) all: 0.506 / Rrim(I) all: 0.996 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
autoPROCdata scaling
BUCCANEERmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: I23 Partial Model

Resolution: 1.51→21.9 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.083 / SU Rfree Blow DPI: 0.085 / SU Rfree Cruickshank DPI: 0.082
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2023 4.88 %RANDOM
Rwork0.202 ---
obs0.203 41490 98.4 %-
Displacement parametersBiso mean: 37.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.2425 Å20 Å20 Å2
2--0.1091 Å20 Å2
3---0.1334 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 1.51→21.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 7 177 2180
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013980HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.017169HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d896SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes582HARMONIC5
X-RAY DIFFRACTIONt_it3980HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion16.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion268SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4472SEMIHARMONIC4
LS refinement shellResolution: 1.51→1.55 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 115 4.1 %
Rwork0.223 2689 -
all0.223 2804 -
obs--90.66 %

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