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- PDB-8s9w: Murine S100A7/S100A15 in presence of calcium -

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Basic information

Entry
Database: PDB / ID: 8s9w
TitleMurine S100A7/S100A15 in presence of calcium
ComponentsProtein S100-A15A
KeywordsMETAL BINDING PROTEIN / EF-Hand / Calcium binding protein / Nutritional immunity / Transition metal binding protein
Function / homology
Function and homology information


zinc ion sequestering activity / RAGE receptor binding / chemoattractant activity / transition metal ion binding / calcium-dependent protein binding / : / inflammatory response / calcium ion binding / endoplasmic reticulum / extracellular space ...zinc ion sequestering activity / RAGE receptor binding / chemoattractant activity / transition metal ion binding / calcium-dependent protein binding / : / inflammatory response / calcium ion binding / endoplasmic reticulum / extracellular space / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
S-100 / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / 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
Similarity search - Domain/homology
ACETATE ION / THIOCYANATE ION / Protein S100-A15A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsHarrison, S.A. / Naretto, A. / Balakrishnan, S. / Chazin, W.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI127793 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI101171 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Comparative analysis of the physical properties of murine and human S100A7: Insight into why zinc piracy is mediated by human but not murine S100A7.
Authors: Harrison, S.A. / Naretto, A. / Balakrishnan, S. / Perera, Y.R. / Chazin, W.J.
History
DepositionMar 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein S100-A15A
B: Protein S100-A15A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,54517
Polymers23,7812
Non-polymers76415
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-126 kcal/mol
Surface area9760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.540, 68.400, 85.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protein S100-A15A / Protein S100-A7A / S100 calcium-binding protein A15A / S100 calcium-binding protein A7A


Mass: 11890.599 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: S100a15a, S100a15, S100a7, S100a7a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6S5I3

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Non-polymers , 6 types, 95 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.94 Å3/Da / Density % sol: 36.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M of Potassium thiocyanate, 20% PEG MME 2K and 0.01M L-Proline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.69→34.16 Å / Num. obs: 21458 / % possible obs: 99.7 % / Redundancy: 13 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.7
Reflection shellResolution: 1.69→1.73 Å / Mean I/σ(I) obs: 1.65 / Num. unique obs: 19412 / CC1/2: 0.81 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
MoRDaphasing
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→23.19 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.432 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23611 1088 5.1 %RANDOM
Rwork0.18561 ---
obs0.18823 20313 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.697 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å20 Å2
2--2.27 Å2-0 Å2
3----4.12 Å2
Refinement stepCycle: 1 / Resolution: 1.69→23.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 37 80 1681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131630
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171446
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.6472188
X-RAY DIFFRACTIONr_angle_other_deg1.4281.5763339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5945191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.44522.04198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75715268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2161511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021815
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02370
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9643.903774
X-RAY DIFFRACTIONr_mcbond_other2.9263.869765
X-RAY DIFFRACTIONr_mcangle_it3.8485.784954
X-RAY DIFFRACTIONr_mcangle_other3.8465.791955
X-RAY DIFFRACTIONr_scbond_it4.3634.445856
X-RAY DIFFRACTIONr_scbond_other4.2894.425850
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2726.441227
X-RAY DIFFRACTIONr_long_range_B_refined7.66847.5261957
X-RAY DIFFRACTIONr_long_range_B_other7.61547.4141943
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.69→1.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 72 -
Rwork0.399 1448 -
obs--99.15 %

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