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- PDB-1f4o: CRYSTAL STRUCTURE OF GRANCALCIN WITH BOUND CALCIUM -

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Basic information

Entry
Database: PDB / ID: 1f4o
TitleCRYSTAL STRUCTURE OF GRANCALCIN WITH BOUND CALCIUM
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: 2.5 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 Ca2+-binding protein 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_conn.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRANCALCIN
B: GRANCALCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5283
Polymers37,4882
Non-polymers401
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-28 kcal/mol
Surface area15530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.370, 50.320, 77.560
Angle α, β, γ (deg.)90.00, 108.17, 90.00
Int Tables number5
Space group name H-MC121

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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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: PEG8000, Glycerol, Calcium chloride, Hepes, pH 7.5, VAPOR DIFFUSION, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl1drop
22 mMdithiothreitol1drop
30.5 mMPMSF1drop
45 mMEGTA1drop
5100 mMHEPES1reservoir
615 %glycerol1reservoir
710-15 %(w/v)PEG80001reservoir
85 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.007
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 12535 / Num. obs: 12026 / % possible obs: 96.2 % / Redundancy: 2.6 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.6
Reflection shellResolution: 2.5→20 Å / Rmerge(I) obs: 0.325 / Num. unique all: 448 / % possible all: 95.9
Reflection
*PLUS
Num. measured all: 31679
Reflection shell
*PLUS
Lowest resolution: 2.53 Å / % possible obs: 95.9 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1191 -random
Rwork0.228 ---
all-12533 --
obs-11533 92 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2630 0 1 53 2684
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.22
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.6 Å2

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