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- PDB-4pe1: Crystal Structure of Calcium-loaded S100B bound to SC124 -

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Basic information

Entry
Database: PDB / ID: 4pe1
TitleCrystal Structure of Calcium-loaded S100B bound to SC124
ComponentsProtein S100-B
KeywordsMETAL BINDING PROTEIN/INHIBITOR / malignant melanoma / calcium binding / complex / covalent inhibitor / 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 / regulation of neuronal synaptic plasticity / ruffle / positive regulation of neuron differentiation / astrocyte activation / axonogenesis / tau protein binding / memory / calcium-dependent protein binding / regulation of translation / learning or memory / positive regulation of canonical NF-kappaB signal transduction / cell adhesion / ciliary basal body / neuronal cell body / positive regulation of cell population proliferation / calcium ion binding / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / extracellular region / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
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
DIETHYLCARBAMODITHIOIC ACID / Protein S100-B
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.576 Å
AuthorsCavalier, M.C. / Pierce, A.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 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Sep 13, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_symm_contact
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_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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
Revision 1.6Oct 23, 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
A: Protein S100-B
B: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8238
Polymers21,3642
Non-polymers4596
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-78 kcal/mol
Surface area9650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.649, 56.463, 48.269
Angle α, β, γ (deg.)90.000, 110.100, 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-DCD / DIETHYLCARBAMODITHIOIC ACID


Mass: 149.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NS2
#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.: 173 / 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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 40% 2-methyl-2,4-pentanediol, 0.1M Hepes,7.5mM CaCl2, 4mM SC124

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.576→35.347 Å / Num. all: 23617 / Num. obs: 23617 / % possible obs: 97.8 % / Redundancy: 3.5 % / Rpim(I) all: 0.018 / Rrim(I) all: 0.034 / Rsym value: 0.029 / Net I/av σ(I): 11.77 / Net I/σ(I): 22.6 / Num. measured all: 83472
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.58-1.662.90.3252.4912031150.2290.3253.589.1
1.66-1.763.70.2213.51200132830.1340.2215.999.5
1.76-1.883.70.1256.21144931160.0760.1259.899.7
1.88-2.033.70.06711.41072629200.0410.06716.599.5
2.03-2.233.70.0418.3972326580.0240.0425.499.6
2.23-2.493.60.0322.4882524230.0190.0332.299.4
2.49-2.883.60.02525.3779521460.0150.02539.698.5
2.88-3.523.50.02423.7630817790.0150.02446.398.8
3.52-4.983.50.02225.7486013990.0140.02251.398.7
4.98-35.3473.40.02521.926657780.0160.0255198

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Processing

Software
NameVersionClassification
SCALA3.3.20data 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: 1.576→35.347 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 1201 5.09 %
Rwork0.2131 22391 -
obs0.2152 23592 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.1 Å2 / Biso mean: 28.9213 Å2 / Biso min: 13.27 Å2
Refinement stepCycle: final / Resolution: 1.576→35.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1445 0 20 173 1638
Biso mean--44.54 37.36 -
Num. residues----179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021506
X-RAY DIFFRACTIONf_angle_d1.0462033
X-RAY DIFFRACTIONf_chiral_restr0.072215
X-RAY DIFFRACTIONf_plane_restr0.003256
X-RAY DIFFRACTIONf_dihedral_angle_d16.704564
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5763-1.63940.32481220.28972123224586
1.6394-1.7140.3151260.27582536266299
1.714-1.80440.33621330.26422525265899
1.8044-1.91740.3691370.260125302667100
1.9174-2.06540.29751330.23642533266699
2.0654-2.27320.26421290.216625422671100
2.2732-2.60210.25481420.21562512265499
2.6021-3.2780.2671220.20872548267098
3.278-35.35620.20721570.18762542269998

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