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- PDB-3gk4: X-ray structure of bovine SBi523,Ca(2+)-S100B -

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Basic information

Entry
Database: PDB / ID: 3gk4
TitleX-ray structure of bovine SBi523,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-53A / Protein S100-B
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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
X: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1674
Polymers10,6821
Non-polymers4853
Water72140
1
X: Protein S100-B
hetero molecules

X: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3338
Polymers21,3642
Non-polymers9696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)34.459, 89.532, 59.234
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 / 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-53A / ethyl 5-{[(1R)-1-(ethoxycarbonyl)-2-oxopropyl]sulfanyl}-1,2-dihydro[1,2,3]triazolo[1,5-a]quinazoline-3-carboxylate


Mass: 404.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N4O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 35% PEGMME550, 7.5mM CaCl2, 100mM Bis-Tris buffer, 2.5% Glycerol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 7056 / % possible obs: 93.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.037 / Χ2: 1.058 / Net I/σ(I): 44.176
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.973.60.2734730.847164.8
1.97-2.054.80.2435990.937180.6
2.05-2.145.60.1716991.016195.4
2.14-2.256.50.1227331.065199.2
2.25-2.396.90.17491.151199.7
2.39-2.587.10.0687401.1831100
2.58-2.847.10.0527661.1351100
2.84-3.2570.057441.025199.9
3.25-4.096.80.0347610.934199.1
4.09-506.50.0247921.06195.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.24 Å32.16 Å
Translation2.24 Å32.16 Å

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Processing

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

1mho


Resolution: 1.9→44.77 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.24 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.818 / SU B: 8.279 / SU ML: 0.126 / SU R Cruickshank DPI: 0.214 / SU Rfree: 0.172 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 326 4.6 %RANDOM
Rwork0.209 ---
obs0.21 7045 93.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.5 Å2 / Biso mean: 47.206 Å2 / Biso min: 37.49 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å20 Å2
2---1.83 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms727 0 30 40 797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022768
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9971029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.069589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99926.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60115145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.574151
X-RAY DIFFRACTIONr_chiral_restr0.1330.2109
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02577
X-RAY DIFFRACTIONr_nbd_refined0.2330.2382
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2534
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.231
X-RAY DIFFRACTIONr_metal_ion_refined0.1380.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.212
X-RAY DIFFRACTIONr_mcbond_it0.7631.5459
X-RAY DIFFRACTIONr_mcangle_it1.1442714
X-RAY DIFFRACTIONr_scbond_it1.9793376
X-RAY DIFFRACTIONr_scangle_it3.1734.5315
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 11 -
Rwork0.226 317 -
all-328 -
obs--60.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
124.7486-3.279-3.104733.680110.38689.32230.0441-1.26570.3560.02360.3986-2.03-0.23650.7587-0.4426-0.17750.04260.0391-0.06950.0247-0.02573.25475.56-2.4199
25.126511.0537-0.193557.21792.45630.2547-0.20510.2758-0.1533-1.23830.192-0.59730.12820.25940.0130.04660.07730.0143-0.12620.0077-0.2168-1.7155-5.6025-6.7581
37.0384-0.36890.62576.6914-0.06466.6023-0.06810.4856-0.4584-0.71020.05390.02340.5881-0.00750.0142-0.05220.0061-0.0165-0.1795-0.027-0.163-5.4413-16.4793-4.8671
48.44482.18592.19086.8593-0.7484.81170.2063-0.3437-0.0340.4743-0.19760.52820.4613-0.1837-0.0087-0.0682-0.01650.0367-0.1558-0.0282-0.1316-10.4705-17.1985.4103
55.32735.48982.445215.61968.037112.5952-0.05620.4020.1435-0.81020.31820.4363-0.2044-0.2012-0.262-0.15160.0174-0.072-0.17120.0258-0.0406-12.6237-8.6122-3.4917
68.2611-5.14988.86478.8866.737637.6814-0.2095-0.80990.2661.02380.4621-0.1791-0.22510.5464-0.2526-0.00220.03240.0334-0.05680.02130.0105-7.181-1.647612.2504
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X1 - 5
2X-RAY DIFFRACTION2X6 - 16
3X-RAY DIFFRACTION3X17 - 40
4X-RAY DIFFRACTION4X41 - 63
5X-RAY DIFFRACTION5X64 - 78
6X-RAY DIFFRACTION6X79 - 88

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