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- PDB-1ggz: CRYSTAL STRUCTURE OF THE CALMODULIN-LIKE PROTEIN (HCLP) FROM HUMA... -

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Basic information

Entry
Database: PDB / ID: 1ggz
TitleCRYSTAL STRUCTURE OF THE CALMODULIN-LIKE PROTEIN (HCLP) FROM HUMAN EPITHELIAL CELLS
ComponentsCALMODULIN-RELATED PROTEIN NB-1
KeywordsMETAL BINDING PROTEIN / Ca+2 binding protein / EF hand
Function / homology
Function and homology information


calcium ion binding / extracellular exosome / cytoplasm
Similarity search - Function
EF hand / : / 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 / : / 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
Calmodulin-like protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsHan, B.-G. / Han, M. / Sui, H. / Yaswen, P. / Walian, P.J. / Jap, B.K.
CitationJournal: FEBS Lett. / Year: 2002
Title: Crystal structure of human calmodulin-like protein: insights into its functional role.
Authors: Han, B.G. / Han, M. / Sui, H. / Yaswen, P. / Walian, P.J. / Jap, B.K.
History
DepositionOct 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: CALMODULIN-RELATED PROTEIN NB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9395
Polymers16,7791
Non-polymers1604
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.38, 93.63, 24.86
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CALMODULIN-RELATED PROTEIN NB-1 / CALMODULIN-LIKE PROTEIN


Mass: 16778.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: EPITHELIAL / Plasmid: PET-11D / Production host: Escherichia coli (E. coli) / References: UniProt: P27482
#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


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.2 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 4.5
Details: MPD, Sodium Acetate, Ethanol, CaCl2, pH 4.5, EVAPORATION, temperature 277K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17 mg/mlprotein1drop
250 mMTris1droppH7.5
32 mM1dropCaCl2
427 %MPD1reservoir
515 %ethanol1reservoir
650 mM1reservoirCaCl2
70.1 Msodium acetate1reservoirpH4.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 24588 / Num. obs: 23940 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 30.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.58 % / Rmerge(I) obs: 0.21 / Num. unique all: 944 / % possible all: 78.7
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 97.7 % / Redundancy: 5.57 % / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
Highest resolution: 1.5 Å / % possible obs: 78.7 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 5

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.5→20 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.221 1153 -
Rwork0.183 --
all-24588 -
obs-23750 96.7 %
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1138 0 4 260 1402
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.033
X-RAY DIFFRACTIONc_angle_deg2.6
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.183 / Rfactor Rfree: 0.221 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0097
X-RAY DIFFRACTIONc_angle_deg1.64

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