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- PDB-1k8u: CRYSTAL STRUCTURE OF CALCIUM-FREE (OR APO) HUMAN S100A6; CYS3MET ... -

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Basic information

Entry
Database: PDB / ID: 1k8u
TitleCRYSTAL STRUCTURE OF CALCIUM-FREE (OR APO) HUMAN S100A6; CYS3MET MUTANT (SELENOMETHIONINE DERIVATIVE)
ComponentsS100A6
KeywordsSIGNALING PROTEIN / S100A6 / CALCYCLIN / CALCIUM REGULATORY PROTEIN / CALCIUM FREE / APO / CACY
Function / homology
Function and homology information


monoatomic ion transmembrane transporter activity / S100 protein binding / tropomyosin binding / ruffle / axonogenesis / cytoplasmic side of plasma membrane / calcium-dependent protein binding / positive regulation of fibroblast proliferation / nuclear envelope / collagen-containing extracellular matrix ...monoatomic ion transmembrane transporter activity / S100 protein binding / tropomyosin binding / ruffle / axonogenesis / cytoplasmic side of plasma membrane / calcium-dependent protein binding / positive regulation of fibroblast proliferation / nuclear envelope / collagen-containing extracellular matrix / calcium ion binding / perinuclear region of cytoplasm / signal transduction / protein homodimerization activity / extracellular exosome / zinc ion binding / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.15 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 25, 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: Derived calculations / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S100A6


Theoretical massNumber of molelcules
Total (without water)10,3161
Polymers10,3161
Non-polymers00
Water2,108117
1
A: S100A6

A: S100A6


Theoretical massNumber of molelcules
Total (without water)20,6312
Polymers20,6312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area3020 Å2
ΔGint-24 kcal/mol
Surface area9140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)37.259, 48.113, 83.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological assembly is generated by the two fold axis: x, -y, -z+1

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Components

#1: Protein S100A6 / CALCYCLIN / CACY


Mass: 10315.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) pLYS / References: UniProt: P06703
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.91 Å3/Da / Density % sol: 35.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 28% PEG 1500, 30mM sodium cacodylate, 6% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mMsodium cacodylate1droppH6.5
22.5 mMbeta-mercaptoethanol1drop
34 mML-cysteine1drop
42 mMEGTA1drop
520 mg/mlprotein1drop
628 %PEG15001reservoir
730 mMsodium cacodylate1reservoirpH7.0
86 %glycerol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONAPS 14-BM-D111.02046, 0.97997, 0.94286
SYNCHROTRONAPS 14-BM-D21.02046, 0.97997, 0.94286
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDDec 7, 2000Bent cylindrical Si-mirror (Rh coating)
ADSC QUANTUM 42CCDDec 8, 2000Bent cylindrical Si-mirror (Rh coating)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111) DOUBLE-CRYSTAL MONOCHROMATORMADMx-ray1
2SI(111) DOUBLE-CRYSTAL MONOCHROMATORMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.020461
30.979971
40.942861
ReflectionResolution: 1.15→30 Å / Num. all: 27160 / Num. obs: 25759 / % possible obs: 95.2 % / Redundancy: 14.8 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.7
Reflection shellResolution: 1.15→1.24 Å / Redundancy: 8 % / Rmerge(I) obs: 0.267 / Num. unique all: 4162 / % possible all: 87.6
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 25856 / % possible obs: 88.2 % / Num. measured all: 399427 / Rmerge(I) obs: 0.061 / Biso Wilson estimate: 14.8 Å2
Reflection shell
*PLUS
Rmerge(I) obs: 0.267

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Processing

Software
NameClassification
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.15→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1226 5 %RANDOM
Rwork0.186 ---
all0.186 25759 --
obs0.186 24523 95.2 %-
Refine analyzeLuzzati sigma a obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms709 0 0 117 826
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_d2.5
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d2.07
LS refinement shellResolution: 1.15→1.24 Å / Rfactor Rfree error: 0.09
RfactorNum. reflection% reflection
Rfree0.22 208 -
Rwork0.186 --
obs-4162 87.6 %
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.186 / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg2.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.07
LS refinement shell
*PLUS
Rfactor Rfree: 0.22 / Rfactor Rwork: 0.186

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