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- PDB-1k9k: CRYSTAL STRUCTURE OF CALCIUM BOUND HUMAN S100A6 -

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Basic information

Entry
Database: PDB / ID: 1k9k
TitleCRYSTAL STRUCTURE OF CALCIUM BOUND HUMAN S100A6
ComponentsS100A6
KeywordsSIGNALING PROTEIN / S100A6 / CALCYCLIN / CALCIUM REGULATORY PROTEIN / CALCIUM BOUND / CACY
Function / homology
Function and homology information


monoatomic ion transmembrane transporter activity / S100 protein binding / tropomyosin binding / ruffle / axonogenesis / cytoplasmic side of plasma membrane / positive regulation of fibroblast proliferation / calcium-dependent protein binding / nuclear envelope / : ...monoatomic ion transmembrane transporter activity / S100 protein binding / tropomyosin binding / ruffle / axonogenesis / cytoplasmic side of plasma membrane / positive regulation of fibroblast proliferation / calcium-dependent protein binding / nuclear envelope / : / calcium ion binding / perinuclear region of cytoplasm / signal transduction / protein homodimerization activity / extracellular exosome / extracellular region / zinc ion binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein S100-A6 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...Protein S100-A6 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / 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
BETA-MERCAPTOETHANOL / Protein S100-A6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsOtterbein, L.R. / Dominguez, R.
CitationJournal: Structure / Year: 2002
Title: Crystal structures of S100A6 in the Ca(2+)-free and Ca(2+)-bound states: the calcium sensor mechanism of S100 proteins revealed at atomic resolution.
Authors: Otterbein, L.R. / Kordowska, J. / Witte-Hoffmann, C. / Wang, C.L. / Dominguez, R.
History
DepositionOct 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2002Provider: 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.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.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: S100A6
B: S100A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7048
Polymers20,3872
Non-polymers3176
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-87 kcal/mol
Surface area9380 Å2
MethodPISA
2
A: S100A6
B: S100A6
hetero molecules

A: S100A6
B: S100A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,40816
Polymers40,7754
Non-polymers63312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area9600 Å2
ΔGint-187 kcal/mol
Surface area16750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.610, 58.439, 51.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein S100A6 / CALCYCLIN / CACY


Mass: 10193.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A6 / Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLYS / References: UniProt: P06703
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 20% PEG 5000 MME, 30 mM TRIS-HCL, 8% GLYCEROL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mMsodium cacodylate1droppH6.5
22.5 mMbeta-mercaptoethanol1drop
34 mML-cysteine1drop
46 mM1dropCaCl2
520 mg/mlprotein1drop
620 %PEG5000 MME1reservoir
730 mMTris-HCl1reservoirpH7.8
88 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 2000 / Details: BENT CYLINDRICAL SI- MIRROR (RH COATING)
RadiationMonochromator: SI(III) DOUBLE CRYSTAL MONOCHROMATOR, L1=1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→19.2 Å / Num. all: 17303 / Num. obs: 16853 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 19.27 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 9.9
Reflection shellResolution: 1.75→1.89 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.192 / Num. unique all: 3218 / % possible all: 96.6
Reflection
*PLUS
Num. measured all: 74706 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
Rmerge(I) obs: 0.192

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PSORIASIN S100A7 (PBD # 1PSR)

1psr


Resolution: 1.76→19.2 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.199 851 5 %RANDOM
Rwork0.185 ---
all0.185 17303 --
obs0.185 16825 97 %-
Refine analyzeLuzzati sigma a obs: 0.11 Å
Refinement stepCycle: LAST / Resolution: 1.76→19.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1414 0 12 151 1577
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_dihedral_angle_deg18.79
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shellResolution: 1.76→1.9 Å / Rfactor Rfree error: 0.11
RfactorNum. reflection% reflection
Rfree0.227 147 -
Rwork0.206 --
obs-3019 91.7 %
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.185 / Rfactor Rfree: 0.199 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.227 / Rfactor Rwork: 0.206

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