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- PDB-5dkr: Crystal Structure of Calcium-loaded S100B bound to SBi29 -

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Basic information

Entry
Database: PDB / ID: 5dkr
TitleCrystal Structure of Calcium-loaded S100B bound to SBi29
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 / 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 / phosphorylation / calcium ion binding / positive regulation of cell population proliferation / 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 / 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
Chem-5CZ / Protein S100-B
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.742 Å
AuthorsCavalier, M.C. / Ansari, M.I. / Pierce, A.D. / Wilder, P.T. / McKnight, L.E. / Raman, E.P. / Neau, D.B. / Bezawada, P. / Alasady, M.J. / Varney, K.M. ...Cavalier, M.C. / Ansari, M.I. / Pierce, A.D. / Wilder, P.T. / McKnight, L.E. / Raman, E.P. / Neau, D.B. / Bezawada, P. / Alasady, M.J. / Varney, K.M. / Toth, E.A. / MacKerell Jr., A.D. / Coop, A. / Weber, D.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA154274 United States
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
CitationJournal: J.Med.Chem. / Year: 2016
Title: Small Molecule Inhibitors of Ca(2+)-S100B Reveal Two Protein Conformations.
Authors: Cavalier, M.C. / Ansari, M.I. / Pierce, A.D. / Wilder, P.T. / McKnight, L.E. / Raman, E.P. / Neau, D.B. / Bezawada, P. / Alasady, M.J. / Charpentier, T.H. / Varney, K.M. / Toth, E.A. / ...Authors: Cavalier, M.C. / Ansari, M.I. / Pierce, A.D. / Wilder, P.T. / McKnight, L.E. / Raman, E.P. / Neau, D.B. / Bezawada, P. / Alasady, M.J. / Charpentier, T.H. / Varney, K.M. / Toth, E.A. / MacKerell, A.D. / Coop, A. / Weber, D.J.
History
DepositionSep 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,9348
Polymers21,3642
Non-polymers5706
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-89 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.745, 47.443, 90.343
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 (cattle) / Gene: S100B / Production host: Escherichia coli (E. coli) / References: UniProt: P02638
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-5CZ / 2-[4-(4-carbamimidoylphenoxy)phenyl]-1H-indole-6-carboximidamide


Mass: 369.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19N5O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 40% 2-methyl-2,4-pentanediol; 0.1M Hepes, pH 7.0, 7.5mM CaCl2
Temp details: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127092 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127092 Å / Relative weight: 1
ReflectionResolution: 1.74→33.3 Å / Num. obs: 20972 / % possible obs: 98.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 28.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.033 / Net I/σ(I): 11.8 / Num. measured all: 82661
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.74-1.773.30.8071.231119510.6820.47783.4
9.05-33.33.40.05327.36061790.9910.03494.2

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Processing

Software
NameVersionClassification
Aimless0.1.26data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MHO

1mho


Resolution: 1.742→33.298 Å / FOM work R set: 0.7799 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 1994 9.55 %
Rwork0.2053 18893 -
obs0.2094 20887 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.04 Å2 / Biso mean: 30.22 Å2 / Biso min: 14.5 Å2
Refinement stepCycle: final / Resolution: 1.742→33.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1445 0 33 172 1650
Biso mean--31.58 39.03 -
Num. residues----179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131513
X-RAY DIFFRACTIONf_angle_d1.2172031
X-RAY DIFFRACTIONf_chiral_restr0.082218
X-RAY DIFFRACTIONf_plane_restr0.006265
X-RAY DIFFRACTIONf_dihedral_angle_d15.774564
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 (%)
1.7423-1.78580.33611220.30081175129787
1.7858-1.83410.32941420.2713361478100
1.8341-1.88810.33941380.270413551493100
1.8881-1.9490.32021400.265913471487100
1.949-2.01870.32311450.248313271472100
2.0187-2.09950.29211420.221113481490100
2.0995-2.1950.29921390.226113561495100
2.195-2.31070.28061460.216213501496100
2.3107-2.45540.26311440.20413631507100
2.4554-2.6450.26661450.217813621507100
2.645-2.9110.24671460.202413721518100
2.911-3.33190.24641460.19591368151499
3.3319-4.19650.19521460.17351385153199
4.1965-33.30380.21961530.19631449160298

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