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- PDB-3gk1: X-ray structure of bovine SBi132,Ca(2+)-S100B -

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Basic information

Entry
Database: PDB / ID: 3gk1
TitleX-ray structure of bovine SBi132,Ca(2+)-S100B
ComponentsProtein S100-B
KeywordsMETAL BINDING PROTEIN / EF hand / Alpha helical / Metal-binding / Nucleus
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 / 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-32A / CACODYLATE ION / Protein S100-B
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsCharpentier, T.H. / Weber, D.J. / Toth, E.A.
CitationJournal: Biochemistry / Year: 2009
Title: Small molecules bound to unique sites in the target protein binding cleft of calcium-bound S100B as characterized by nuclear magnetic resonance and X-ray crystallography.
Authors: Charpentier, T.H. / Wilder, P.T. / Liriano, M.A. / Varney, K.M. / Zhong, S. / Coop, A. / Pozharski, E. / MacKerell, A.D. / Toth, E.A. / Weber, D.J.
History
DepositionMar 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1785
Polymers10,6821
Non-polymers4974
Water66737
1
A: Protein S100-B
hetero molecules

A: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,35710
Polymers21,3642
Non-polymers9938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3010 Å2
ΔGint-75 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.666, 90.778, 58.994
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-132-

HOH

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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: 10681.974 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: S100B / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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-32A / 2-[(5-hex-1-yn-1-ylfuran-2-yl)carbonyl]-N-methylhydrazinecarbothioamide


Mass: 279.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17N3O2S
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 28% PEG3350, 7.5mM CaCl2, 100mM Cacodylate buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→45.41 Å / Num. obs: 5585 / % possible obs: 97.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.042 / Χ2: 1.093 / Net I/σ(I): 37.481
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.183.80.2775250.984193.8
2.18-2.265.30.1995380.908198.7
2.26-2.376.30.1635580.9991100
2.37-2.496.80.1065611.0261100
2.49-2.657.10.085641.011100
2.65-2.857.10.0595691.2351100
2.85-3.147.10.0515641.2631100
3.14-3.5970.0485671.094199.8
3.59-4.526.70.0375871.222199.7
4.52-456.20.0285521.044188.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å22.8 Å
Translation2.5 Å22.8 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MHO

1mho


Resolution: 2.1→45.41 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.29 / WRfactor Rwork: 0.249 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.797 / SU B: 14.437 / SU ML: 0.17 / SU R Cruickshank DPI: 0.295 / SU Rfree: 0.231 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.261 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 251 4.5 %RANDOM
Rwork0.206 5321 --
obs0.208 5572 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.86 Å2 / Biso mean: 46.161 Å2 / Biso min: 35.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2---0.42 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms710 0 26 37 773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022744
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.982994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.209587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58826.4139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66815140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.951151
X-RAY DIFFRACTIONr_chiral_restr0.1220.2107
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02553
X-RAY DIFFRACTIONr_nbd_refined0.2160.2292
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2510
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.232
X-RAY DIFFRACTIONr_metal_ion_refined0.1860.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3090.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.28
X-RAY DIFFRACTIONr_mcbond_it0.7621.5451
X-RAY DIFFRACTIONr_mcangle_it1.092698
X-RAY DIFFRACTIONr_scbond_it2.3773322
X-RAY DIFFRACTIONr_scangle_it3.7294.5296
LS refinement shellResolution: 2.102→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 15 -
Rwork0.277 358 -
all-373 -
obs--88.81 %
Refinement TLS params.Method: refined / Origin x: 7.3111 Å / Origin y: 11.2699 Å / Origin z: 0.0091 Å
111213212223313233
T-0.0939 Å20.0578 Å20.0237 Å2--0.0707 Å2-0.0156 Å2---0.1272 Å2
L3.4146 °21.5802 °20.2468 °2-8.3282 °20.7299 °2--1.6014 °2
S0.0623 Å °-0.0274 Å °0.0204 Å °-0.3071 Å °-0.0978 Å °-0.1568 Å °-0.2201 Å °-0.0408 Å °0.0355 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 88
2X-RAY DIFFRACTION1A96 - 132

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