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- PDB-4pe0: Crystal Structure of Calcium-loaded S100B bound to SBi4434 -

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Basic information

Entry
Database: PDB / ID: 4pe0
TitleCrystal Structure of Calcium-loaded S100B bound to SBi4434
ComponentsProtein S100-B
KeywordsMETAL BINDING PROTEIN/INHIBITOR / malignant melanoma / Calcium binding / covalent inhibitor / complex / METAL BINDING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


Advanced glycosylation endproduct receptor signaling / TRAF6 mediated NF-kB activation / TAK1-dependent IKK and NF-kappa-B activation / adaptive thermogenesis / kinase inhibitor activity / sympathetic neuron projection extension / positive regulation of complement activation / RAGE receptor binding / negative regulation of monocyte chemotactic protein-1 production / S100 protein binding ...Advanced glycosylation endproduct receptor signaling / TRAF6 mediated NF-kB activation / TAK1-dependent IKK and NF-kappa-B activation / adaptive thermogenesis / kinase inhibitor activity / sympathetic neuron projection extension / positive regulation of complement activation / RAGE receptor binding / negative regulation of monocyte chemotactic protein-1 production / S100 protein binding / phosphorylation / axonogenesis / astrocyte activation / tau protein binding / calcium-dependent protein binding / regulation of translation / positive regulation of canonical NF-kappaB signal transduction / learning or memory / cell adhesion / positive regulation of cell population proliferation / calcium ion binding / protein homodimerization activity / extracellular space / zinc ion binding / extracellular region / nucleus / 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 domain / 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 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
2-[(2-hydroxyethyl)sulfanyl]naphthalene-1,4-dione / Protein S100-B
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsCavalier, M.C. / Pierce, P.D. / Wilder, P.T. / Neau, D. / Toth, E.A. / Weber, D.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM58888 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA107331 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA154274 United States
CitationJournal: Biochemistry / Year: 2014
Title: Covalent Small Molecule Inhibitors of Ca(2+)-Bound S100B.
Authors: Cavalier, M.C. / Pierce, A.D. / Wilder, P.T. / Alasady, M.J. / Hartman, K.G. / Neau, D.B. / Foley, T.L. / Jadhav, A. / Maloney, D.J. / Simeonov, A. / Toth, E.A. / Weber, D.J.
History
DepositionApr 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,9938
Polymers21,3642
Non-polymers6296
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-80 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.180, 56.270, 48.050
Angle α, β, γ (deg.)90.000, 108.790, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 10681.974 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: S100B / Production host: Escherichia coli (E. coli) / References: UniProt: P02638
#2: Chemical ChemComp-NQS / 2-[(2-hydroxyethyl)sulfanyl]naphthalene-1,4-dione


Mass: 234.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10O3S
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 40% 2-methyl-2,4-pentanediol, 0.1M Cacodylate, 7.5mM CaCl2, 4mM SBi4434

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.08→21.69 Å / Num. obs: 70592 / % possible obs: 92.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 9.32 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.046 / Net I/σ(I): 9 / Num. measured all: 244228 / Scaling rejects: 81
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.08-1.13.50.40231212635040.25393
5.9-21.692.90.08315.12961020.05319.7

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Processing

Software
NameVersionClassification
Aimless0.1.26data scaling
Blu-Icedata collection
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MHO

1mho


Resolution: 1.08→14.641 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2111 2006 2.84 %
Rwork0.1917 68572 -
obs0.1923 70578 92.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 44.89 Å2 / Biso mean: 14.8984 Å2 / Biso min: 5.02 Å2
Refinement stepCycle: final / Resolution: 1.08→14.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1464 0 54 321 1839
Biso mean--22.03 25.09 -
Num. residues----181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151552
X-RAY DIFFRACTIONf_angle_d1.1332126
X-RAY DIFFRACTIONf_chiral_restr0.066217
X-RAY DIFFRACTIONf_plane_restr0.005262
X-RAY DIFFRACTIONf_dihedral_angle_d14.424561
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.08-1.10390.33381570.27174956511393
1.1039-1.13380.2631430.24464954509794
1.1338-1.16710.27871440.22424984512895
1.1671-1.20480.21131470.21335007515495
1.2048-1.24780.21661490.20675047519695
1.2478-1.29770.24211420.20225059520196
1.2977-1.35680.19561420.19825091523396
1.3568-1.42820.22581560.18975057521396
1.4282-1.51760.20461530.17925109526296
1.5176-1.63470.18641460.17435138528497
1.6347-1.79890.2171540.17645223537798
1.7989-2.05860.18421450.17375121526696
2.0586-2.59130.17281450.16664819496491
2.5913-14.64220.264830.22663007309055

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