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- PDB-3hcm: Crystal structure of human S100B in complex with S45 -

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Basic information

Entry
Database: PDB / ID: 3hcm
TitleCrystal structure of human S100B in complex with S45
ComponentsProtein S100-B
KeywordsMETAL BINDING PROTEIN / S100B / calcium binding protein / inhibitor / Calcium / Cytoplasm / Metal-binding / Nucleus
Function / homology
Function and homology information


adaptive thermogenesis / sympathetic neuron projection extension / RAGE receptor binding / ion binding / S100 protein binding / regulation of neuronal synaptic plasticity / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / Nuclear signaling by ERBB4 / ruffle ...adaptive thermogenesis / sympathetic neuron projection extension / RAGE receptor binding / ion binding / S100 protein binding / regulation of neuronal synaptic plasticity / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / Nuclear signaling by ERBB4 / ruffle / positive regulation of neuron differentiation / axonogenesis / central nervous system development / tau protein binding / TAK1-dependent IKK and NF-kappa-B activation / memory / calcium-dependent protein binding / positive regulation of canonical NF-kappaB signal transduction / learning or memory / cell adhesion / intracellular membrane-bounded organelle / neuronal cell body / calcium ion binding / positive regulation of cell population proliferation / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein S100-B / 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 / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif ...Protein S100-B / 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 / 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
ACETATE ION / Chem-S45 / Protein S100-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMangani, S. / Cesari, L.
CitationJournal: Chemmedchem / Year: 2010
Title: Fragmenting the S100B-p53 Interaction: Combined Virtual/Biophysical Screening Approaches to Identify Ligands
Authors: Agamennone, M. / Cesari, L. / Lalli, D. / Turlizzi, E. / Del Conte, R. / Turano, P. / Mangani, S. / Padova, A.
History
DepositionMay 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 1, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,2019
Polymers21,4542
Non-polymers7477
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-72 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.257, 57.797, 47.745
Angle α, β, γ (deg.)90.00, 111.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein S100-B / S100 calcium-binding protein B / S-100 protein subunit beta / S-100 protein beta chain


Mass: 10727.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: The protein was purchased from a commercial source.
Production host: Escherichia coli (E. coli) / References: UniProt: P04271
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-S45 / (3R)-3-[3-(4-chlorophenyl)-1,2,4-oxadiazol-5-yl]piperidine


Mass: 263.723 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H14ClN3O
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M sodium acetate, 0.02M calcium chloride, 45% methylpenthanediol, pH4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.814 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Oct 24, 2006
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.814 Å / Relative weight: 1
ReflectionResolution: 2→17.68 Å / Num. all: 12148 / Num. obs: 9406 / % possible obs: 81.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 29.93 Å2 / Rsym value: 0.041 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 9.1 / Num. unique all: 1337 / % possible all: 81.5

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H61

2h61


Resolution: 2→17.63 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.84 / SU B: 5.87 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.365 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31149 457 4.6 %RANDOM
Rwork0.22722 ---
all0.23105 9406 --
obs0.23105 9406 81.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.961 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→17.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1471 0 44 96 1611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211538
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.9782057
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6025181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33626.50683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.14715294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.357152
X-RAY DIFFRACTIONr_chiral_restr0.1150.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021156
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.250.2834
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21046
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.298
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1290.213
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1351.5938
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67821442
X-RAY DIFFRACTIONr_scbond_it2.5333674
X-RAY DIFFRACTIONr_scangle_it3.6454.5614
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 43 -
Rwork0.199 736 -
obs--86.94 %

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