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- PDB-1k94: Crystal structure of des(1-52)grancalcin with bound calcium -

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Basic information

Entry
Database: PDB / ID: 1k94
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 / cytosol / cytoplasm
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: 1.7 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: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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)37,6635
Polymers37,5422
Non-polymers1203
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-28 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.120, 71.130, 77.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 18771.225 Da / Num. of mol.: 2 / 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: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 256 / 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: 1.99 Å3/Da / Density % sol: 38.14 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6
Details: PEG 8000, Calcium acetate, sodium cacodylate, pH 6.0, EVAPORATION at 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 12, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 33645 / Num. obs: 30676 / % possible obs: 91.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.064 / Net I/σ(I): 11.1
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.332 / Rsym value: 0.331 / % possible all: 82.4

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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: 1.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 1492 5.2 %random
Rwork0.2028 ---
all-30050 --
obs-28558 89.3 %-
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2634 0 3 256 2893
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.02

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