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- PDB-3nxa: X-ray structure of the apo form of human S100A16 -

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Basic information

Entry
Database: PDB / ID: 3nxa
TitleX-ray structure of the apo form of human S100A16
ComponentsProtein S100-A16
KeywordsMETAL BINDING PROTEIN / S100 family / calcium binding protein / apo / S100A16 / EF-hand proteins / calcium binding proteins / S100 proteins / protein dynamics
Function / homology
Function and homology information


response to calcium ion / calcium-dependent protein binding / calcium ion binding / nucleolus / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / nucleus ...response to calcium ion / calcium-dependent protein binding / calcium ion binding / nucleolus / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / nucleus / plasma membrane / cytosol
Similarity search - Function
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 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...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 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: 2.1 Å
AuthorsCalderone, V.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2011
Title: Structural characterization of human S100A16, a low-affinity calcium binder.
Authors: Babini, E. / Bertini, I. / Borsi, V. / Calderone, V. / Hu, X. / Luchinat, C. / Parigi, G.
History
DepositionJul 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein S100-A16
B: Protein S100-A16
C: Protein S100-A16
D: Protein S100-A16


Theoretical massNumber of molelcules
Total (without water)46,0484
Polymers46,0484
Non-polymers00
Water1,44180
1
A: Protein S100-A16
B: Protein S100-A16


Theoretical massNumber of molelcules
Total (without water)23,0242
Polymers23,0242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-31 kcal/mol
Surface area11740 Å2
MethodPISA
2
C: Protein S100-A16
D: Protein S100-A16


Theoretical massNumber of molelcules
Total (without water)23,0242
Polymers23,0242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-29 kcal/mol
Surface area10370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.571, 156.571, 38.138
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Protein S100-A16 / S100 calcium-binding protein A16 / Protein S100-F / Aging-associated gene 13 protein


Mass: 11512.035 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AAG13, S100A16, S100F / Plasmid: BL21 Gold / Production host: Escherichia coli (E. coli) / Strain (production host): plasmid / References: UniProt: Q96FQ6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2 M tri-sodium potassium citrate, 20% PEG 3350, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.006 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 28, 2008 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 29230 / Num. obs: 29230 / % possible obs: 91.6 % / Redundancy: 11.7 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 17.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3660 / Rsym value: 0.339 / % possible all: 79.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Previously solved low resolution SAD structure

Resolution: 2.1→39.15 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.898 / SU B: 30.176 / SU ML: 0.304 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29843 2650 9.1 %RANDOM
Rwork0.24762 ---
all0.25233 26551 --
obs0.25233 26551 91.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.498 Å2
Baniso -1Baniso -2Baniso -3
1--42 Å20 Å20 Å2
2---42 Å20 Å2
3---84.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 0 80 3074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0730.0223044
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg4.451.9584087
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6135363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.47325.241145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.54215598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6431511
X-RAY DIFFRACTIONr_chiral_restr0.3770.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0280.022221
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.2641.51820
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.79922933
X-RAY DIFFRACTIONr_scbond_it7.47231224
X-RAY DIFFRACTIONr_scangle_it10.2974.51154
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 173 -
Rwork0.329 1666 -
obs--79.51 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
1-10.550634.391124.1185
2-18.302648.340428.2212
324.168371.846534.6738
48.444669.22437.0617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 102
2X-RAY DIFFRACTION2B4 - 100
3X-RAY DIFFRACTION3C5 - 101
4X-RAY DIFFRACTION4D4 - 98

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