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- PDB-1f4q: CRYSTAL STRUCTURE OF APO GRANCALCIN -

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Basic information

Entry
Database: PDB / ID: 1f4q
TitleCRYSTAL STRUCTURE OF APO GRANCALCIN
ComponentsGRANCALCIN
KeywordsMETAL TRANSPORT / penta-Ef-hand protein / calcium binding protein
Function / homology
Function and homology information


azurophil granule lumen / membrane fusion / protein heterodimerization activity / calcium ion binding / Neutrophil degranulation / protein homodimerization activity / extracellular exosome / extracellular region / plasma membrane / cytoplasm / cytosol
Similarity search - Function
EF hand / EF-hand domain pair / 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 ...EF hand / EF-hand domain pair / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsJia, J. / Han, Q. / Borregaard, N. / Lollike, K. / Cygler, M.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of human grancalcin, a member of the penta-EF-hand protein family.
Authors: Jia, J. / Han, Q. / Borregaard, N. / Lollike, K. / Cygler, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray analysis of human grancalcin, a novel cytosolic Ca2+-binding protein present in leukocytes
Authors: Han, Q. / Jia, J. / Li, Y. / Lollike, K. / Cygler, M.
History
DepositionJun 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GRANCALCIN
B: GRANCALCIN


Theoretical massNumber of molelcules
Total (without water)37,4882
Polymers37,4882
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-17 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.4, 81.1, 46.7
Angle α, β, γ (deg.)90.0, 111.3, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GRANCALCIN


Mass: 18744.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX2T / Production host: Escherichia coli (E. coli) / References: UniProt: P28676
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium acetate, sodium chloride, ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl1drop
22 mMdithiothreitol1drop
30.5 mMPMSF1drop
45 mMEGTA1drop
50.1 Msodium acetate1reservoir
60.1 M1reservoirNaCl
71 Mammonium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.00899
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00899 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 26599 / Num. obs: 25454 / % possible obs: 95.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 14.6
Reflection shellResolution: 1.9→20 Å / Rmerge(I) obs: 0.214 / Num. unique all: 996 / % possible all: 94.1
Reflection
*PLUS
Num. measured all: 96346
Reflection shell
*PLUS
% possible obs: 94.1 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→6 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1997 -Random
Rwork0.213 ---
all-26582 --
obs-25452 95.7 %-
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2603 0 0 175 2778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.02
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 7.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.7 Å2

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