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- PDB-8fj8: Crystal structure of Mn(2+),Ca(2+)-S100B -

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Basic information

Entry
Database: PDB / ID: 8fj8
TitleCrystal structure of Mn(2+),Ca(2+)-S100B
ComponentsProtein S100-B
KeywordsMETAL BINDING PROTEIN / Manganese / Calcium / cancer
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, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...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, 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
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsHunter, D.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM129327 United States
CitationJournal: To Be Published
Title: Structural insights into ions binding to S100A1 versus S100B
Authors: Young, B. / Sevdalis, S. / Weber, D.J. / Hunter, D. / Zhuang, X. / Varney, K. / Melville, Z. / Weber, D.J.
History
DepositionDec 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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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)10,5504
Polymers10,4151
Non-polymers1353
Water41423
1
A: Protein S100-B
hetero molecules

A: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1008
Polymers20,8292
Non-polymers2706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area3240 Å2
ΔGint-91 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.598, 90.602, 58.087
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-221-

HOH

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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: 10414.713 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 29% PEG MME 550, 100mM Cacodylate pH 6.9, 7.5mM CaCl2

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.8843 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8843 Å / Relative weight: 1
ReflectionResolution: 2.17→58.09 Å / Num. obs: 5043 / % possible obs: 98.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 50.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Net I/σ(I): 23.6
Reflection shellResolution: 2.17→2.24 Å / Rmerge(I) obs: 0.598 / Num. unique obs: 1953 / CC1/2: 0.703

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→45.3 Å / SU ML: 0.4505 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.9159
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2569 259 5.19 %
Rwork0.2008 4734 -
obs0.2042 4993 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.65 Å2
Refinement stepCycle: LAST / Resolution: 2.17→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms727 0 3 23 753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089738
X-RAY DIFFRACTIONf_angle_d0.9878987
X-RAY DIFFRACTIONf_chiral_restr0.0482108
X-RAY DIFFRACTIONf_plane_restr0.006129
X-RAY DIFFRACTIONf_dihedral_angle_d5.722591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.730.35271390.2532275X-RAY DIFFRACTION97.34
2.73-45.30.23251200.18972459X-RAY DIFFRACTION98.93
Refinement TLS params.Method: refined / Origin x: 7.28801516472 Å / Origin y: 101.440384636 Å / Origin z: 0.0876225608917 Å
111213212223313233
T0.335014416943 Å20.0499268625056 Å2-0.00363683038462 Å2-0.370303029806 Å20.00300319422581 Å2--0.329408697131 Å2
L3.36250670636 °21.30987520912 °2-0.341908179581 °2-8.07783777374 °21.42824127711 °2--3.08187052221 °2
S-0.0224356178731 Å °0.228950309193 Å °0.0414914888209 Å °-0.505936606609 Å °0.113477963041 Å °-0.300482139803 Å °-0.347128962635 Å °-0.0236865227685 Å °-0.0870702803034 Å °
Refinement TLS groupSelection details: all

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