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- PDB-1k95: Crystal structure of des(1-52)grancalcin with bound calcium -

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Basic information

Entry
Database: PDB / ID: 1k95
TitleCrystal structure of des(1-52)grancalcin with bound calcium
ComponentsGRANCALCIN
KeywordsMETAL BINDING PROTEIN / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJia, J. / Borregaard, N. / Lollike, K. / Cygler, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of Ca(2+)-loaded human grancalcin.
Authors: Jia, J. / Borregaard, N. / Lollike, K. / Cygler, M.
#1: 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.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallizaiton and preliminary X-ray analysis of human grancalcin, a novel Ca2+-binding protein in leukocytes
Authors: Han, Q. / Jia, J. / Li, Y. / Lollike, K. / Cygler, M.
History
DepositionOct 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRANCALCIN


Theoretical massNumber of molelcules
Total (without water)18,7711
Polymers18,7711
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: GRANCALCIN

A: GRANCALCIN


Theoretical massNumber of molelcules
Total (without water)37,5422
Polymers37,5422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area3610 Å2
ΔGint-15 kcal/mol
Surface area14890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.650, 57.650, 154.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Cell settinghexagonal
Space group name H-MP6522

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Components

#1: Protein GRANCALCIN / EF-hand calcium-binding protein


Mass: 18771.225 Da / Num. of mol.: 1 / Fragment: residues 53-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P28676
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 1.98 Å3/Da / Density % sol: 37.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: ammoniun sulfate, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
250 mMTris1droppH7.5
35 mMEGTA1drop
4100 mMsodium acetate1reservoirpH4.5
50.7 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 12769 / Num. obs: 12769 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.083 / Net I/σ(I): 13.5
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.23 / Rsym value: 0.31 / % possible all: 99.3
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 163585
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.23

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F4Q

1f4q


Resolution: 1.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1297 11.5 %Random
Rwork0.2113 ---
all-12729 --
obs-11261 --
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 0 132 1424
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.96
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 11.5 % / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS

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