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- PDB-5er5: Crystal Structure of Calcium-loaded S100B bound to SC1990 -

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Basic information

Entry
Database: PDB / ID: 5er5
TitleCrystal Structure of Calcium-loaded S100B bound to SC1990
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
ETHIDIUM / Protein S100-B
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsCavalier, M.C. / Melville, Z.E. / Aligholizadeh, E. / Fang, L. / Alasady, M.J. / Pierce, A.D. / Wilder, P.T. / MacKerell Jr., A.D. / Weber, D.J.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA107331 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)CA154274 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR007592 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Novel protein-inhibitor interactions in site 3 of Ca(2+)-bound S100B as discovered by X-ray crystallography.
Authors: Cavalier, M.C. / Melville, Z. / Aligholizadeh, E. / Raman, E.P. / Yu, W. / Fang, L. / Alasady, M. / Pierce, A.D. / Wilder, P.T. / MacKerell, A.D. / Weber, D.J.
History
DepositionNov 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0774
Polymers10,6821
Non-polymers3953
Water2,846158
1
A: Protein S100-B
hetero molecules

A: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1538
Polymers21,3642
Non-polymers7896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3650 Å2
ΔGint-83 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.418, 88.279, 59.114
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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.: 1
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.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ET / ETHIDIUM / Ethidium bromide


Mass: 314.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% PEG 3,350; 0.1M Hepes, pH7.0; 5% Glycerol; 7.5mM CaCl2

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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: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.26→35.37 Å / Num. obs: 25238 / % possible obs: 99.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 14.99 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.014 / Rrim(I) all: 0.036 / Net I/σ(I): 28.7 / Num. measured all: 173942
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.26-1.285.41.038630111720.5310.4851.151.694.3
6.9-35.375.70.02610601870.9990.0120.0299399.5

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Processing

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

1mho


Resolution: 1.26→35.368 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1868 2000 7.93 %
Rwork0.1524 23218 -
obs0.1551 25218 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.48 Å2 / Biso mean: 20.6095 Å2 / Biso min: 10.38 Å2
Refinement stepCycle: final / Resolution: 1.26→35.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms727 0 26 158 911
Biso mean--19.93 35.58 -
Num. residues----90
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009765
X-RAY DIFFRACTIONf_angle_d1.0181026
X-RAY DIFFRACTIONf_chiral_restr0.376108
X-RAY DIFFRACTIONf_plane_restr0.005131
X-RAY DIFFRACTIONf_dihedral_angle_d20.109282
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 (%)
1.2597-1.29120.28371330.23661550168395
1.2912-1.32610.24881410.20071635177698
1.3261-1.36510.21941400.18421621176198
1.3651-1.40920.20561390.16251619175898
1.4092-1.45950.23111430.15241648179199
1.4595-1.5180.1751420.12881653179599
1.518-1.58710.15321410.12041640178199
1.5871-1.67070.18291420.11481647178999
1.6707-1.77540.1681440.126616751819100
1.7754-1.91250.18881430.123716531796100
1.9125-2.10490.15791450.123816841829100
2.1049-2.40940.15841450.126616841829100
2.4094-3.03540.1721480.157817181866100
3.0354-35.38170.20541540.178617911945100

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