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- PDB-3gk2: X-ray structure of bovine SBi279,Ca(2+)-S100B -

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Basic information

Entry
Database: PDB / ID: 3gk2
TitleX-ray structure of bovine SBi279,Ca(2+)-S100B
ComponentsProtein S100-B
KeywordsMETAL BINDING PROTEIN / EF hand / Alpha helical / Metal-binding / Nucleus
Function / homology
Function and homology information


kinase inhibitor activity / positive regulation of complement activation / negative regulation of monocyte chemotactic protein-1 production / S100 protein binding / RAGE receptor binding / regulation of neuronal synaptic plasticity / astrocyte activation / phosphorylation / axonogenesis / ruffle ...kinase inhibitor activity / positive regulation of complement activation / negative regulation of monocyte chemotactic protein-1 production / S100 protein binding / RAGE receptor binding / regulation of neuronal synaptic plasticity / astrocyte activation / phosphorylation / axonogenesis / ruffle / tau protein binding / memory / calcium-dependent protein binding / regulation of translation / positive regulation of I-kappaB kinase/NF-kappaB signaling / learning or memory / neuronal cell body / calcium ion binding / positive regulation of cell population proliferation / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein S100-B / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / S100/CaBP-9k-type, calcium binding, subdomain / 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 / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / S100/CaBP-9k-type, calcium binding, subdomain / 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-27A / CACODYLATE ION / Protein S100-B
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.984 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 / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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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)11,1775
Polymers10,6821
Non-polymers4954
Water59433
1
A: Protein S100-B
hetero molecules

A: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,35310
Polymers21,3642
Non-polymers9898
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2940 Å2
ΔGint-79 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.224, 91.158, 58.649
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-27A / (Z)-2-[2-(4-methylpiperazin-1-yl)benzyl]diazenecarbothioamide


Mass: 277.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N5S
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


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


Mass: 18.015 Da / Num. of mol.: 33 / 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: 42.55 %
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: 1.984→45.6 Å / Num. obs: 6299 / % possible obs: 95.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.049 / Χ2: 1.101 / Net I/σ(I): 27.849
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.984-2.073.80.2334871.011177.2
2.07-2.154.70.2446101.245191.9
2.15-2.255.70.1426111.163197.3
2.25-2.376.50.1556481.163199.5
2.37-2.526.90.0946571.0881100
2.52-2.717.10.0736561.1181100
2.71-2.997.10.0616501.0421100
2.99-3.4270.066651.0641100
3.42-4.316.90.0476781.073199.7
4.31-456.40.0326371.068188.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.04 Å
Translation2.5 Å32.04 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
Resolution: 1.984→45.6 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.303 / WRfactor Rwork: 0.271 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.74 / SU B: 15.929 / SU ML: 0.176 / SU R Cruickshank DPI: 0.249 / SU Rfree: 0.207 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.281 291 4.6 %RANDOM
Rwork0.227 5993 --
obs0.229 6284 94.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.74 Å2 / Biso mean: 50.578 Å2 / Biso min: 41.15 Å2
Baniso -1Baniso -2Baniso -3
1-2.54 Å20 Å20 Å2
2---2.17 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.984→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms710 0 26 33 769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022745
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.986997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.813587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27826.4139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54715140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.855151
X-RAY DIFFRACTIONr_chiral_restr0.0580.2107
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02561
X-RAY DIFFRACTIONr_nbd_refined0.1930.2305
X-RAY DIFFRACTIONr_nbtor_refined0.2930.2509
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.229
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.070.27
X-RAY DIFFRACTIONr_mcbond_it0.11.5450
X-RAY DIFFRACTIONr_mcangle_it0.1592698
X-RAY DIFFRACTIONr_scbond_it0.3163326
X-RAY DIFFRACTIONr_scangle_it0.5184.5299
LS refinement shellResolution: 1.984→2.035 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 9 -
Rwork0.321 285 -
all-294 -
obs--59.88 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.66476.236413.084862.8445-13.747137.5394-0.057-0.32320.57910.37490.46692.5121-0.0982-1.7425-0.4099-0.13660.0424-0.0589-0.1165-0.05740.0335-3.13-5.6095-2.5475
23.624813.3126-1.954751.1012-7.15571.0544-0.29190.36710.0347-0.48030.46070.6822-0.6324-0.8096-0.16880.06690.0562-0.0819-0.1586-0.0233-0.19431.75235.8113-6.7006
37.8439-0.2828-2.9276.83920.29419.9287-0.03720.45620.4186-0.89630.0070.1919-0.4163-0.05560.0302-0.02070.061-0.018-0.2199-0.0044-0.20125.547216.7001-4.8596
47.81212.1654-2.69627.9721.01515.56090.2585-0.53170.05710.2637-0.2202-0.2965-0.3990.0553-0.0383-0.12860.0207-0.0257-0.1420.0245-0.171310.605717.47615.4754
54.74961.4604-1.046512.2918-5.717510.81980.02560.3079-0.2166-0.83430.2935-0.37540.17710.1794-0.3191-0.09810.0060.0708-0.2291-0.0508-0.113912.92938.8272-3.518
63.67499.4904-11.057124.8003-30.612147.8040.1309-0.8092-0.13871.23380.2675-0.2751-0.5214-0.9075-0.39840.01460.09080.0068-0.0268-0.0656-0.05227.59981.720311.8054
71.58510.6608-0.09881.26620.84111.80630.1579-0.03110.0067-0.1537-0.01910.0158-0.17930.0046-0.1387-0.05310.05720.0504-0.0802-0.0004-0.01278.596815.33780.7777
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION2A6 - 16
3X-RAY DIFFRACTION3A17 - 40
4X-RAY DIFFRACTION4A41 - 63
5X-RAY DIFFRACTION5A64 - 78
6X-RAY DIFFRACTION6A79 - 88
7X-RAY DIFFRACTION7A96 - 128

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