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- PDB-1k9p: CRYSTAL STRUCTURE OF CALCIUM FREE (OR APO) HUMAN S100A6 -

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Basic information

Entry
Database: PDB / ID: 1k9p
TitleCRYSTAL STRUCTURE OF CALCIUM FREE (OR APO) HUMAN S100A6
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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: Derived calculations / 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 / struct_conn / struct_site
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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2722
Polymers10,1941
Non-polymers781
Water1,27971
1
A: S100A6
hetero molecules

A: S100A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5444
Polymers20,3872
Non-polymers1562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area3290 Å2
ΔGint-31 kcal/mol
Surface area9060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)37.444, 47.982, 82.984
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: 10193.729 Da / Num. of mol.: 1
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-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 1.86 Å3/Da / Density % sol: 33.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 28% PEG 1500, 30 mM SODIUM CACODYLATE, 6% GLYCEROL,EGTA 2MM, 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54189 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 4, 1998 / Details: CHARLES SUPPER DOUBLE MIRROR X-RAY FOCUSING SYSTEM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.541891
211
ReflectionResolution: 1.9→30 Å / Num. all: 6148 / Num. obs: 6136 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 6 % / Rmerge(I) obs: 0.087 / Num. unique all: 1509 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. measured all: 40635 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
Rmerge(I) obs: 0.087

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CALCIUM FREE S100A6 CYS3MET MUTANT (SELENOMETHIONINE DERIVATIVE)(PDB # 1K8U)

1k8u


Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.182 314 5 %RANDOM
Rwork0.176 ---
all0.176 6148 --
obs0.176 6130 99.8 %-
Refine analyzeLuzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms707 0 4 71 782
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_dihedral_angle_deg19.84
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.042
RfactorNum. reflection% reflection
Rfree0.216 54 -
Rwork0.199 --
obs-1130 95.5 %
Refinement
*PLUS
Highest resolution: 1.9 Å / % reflection Rfree: 5 % / Rfactor obs: 0.176 / Rfactor Rfree: 0.182 / Rfactor Rwork: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.216 / Rfactor Rwork: 0.199

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