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- PDB-3lle: X-ray structure of bovine SC0322,Ca(2+)-S100B -

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Basic information

Entry
Database: PDB / ID: 3lle
TitleX-ray structure of bovine SC0322,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 / 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
Chem-SGE / Protein S100-B
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsCharpentier, T.H. / Weber, D.J. / Wilder, P.W.
CitationJournal: Int.J.High Throughput Screen / Year: 2010
Title: In vitro screening and structural characterization of inhibitors of the S100B-p53 interaction.
Authors: Wilder, P.T. / Charpentier, T.H. / Liriano, M.A. / Gianni, K. / Varney, K.M. / Pozharski, E. / Coop, A. / Toth, E.A. / Mackerell, A.D. / Weber, D.J.
History
DepositionJan 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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
B: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1918
Polymers21,3642
Non-polymers8276
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-87 kcal/mol
Surface area9480 Å2
MethodPISA
2
A: Protein S100-B
B: Protein S100-B
hetero molecules

A: Protein S100-B
B: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,38216
Polymers42,7284
Non-polymers1,65412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8470 Å2
ΔGint-184 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.267, 46.267, 172.413
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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.: 2
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.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SGE / 13-methyl-13,14-dihydro[1,3]benzodioxolo[5,6-c][1,3]dioxolo[4,5-i]phenanthridine / Dihydrosanguinarine


Mass: 333.337 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H15NO4 / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG3350, CaCl2, Li2SO4, Cacodylate buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.8 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 19198 / % possible obs: 99.4 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.055 / Χ2: 1.033 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.926.40.51918080.94296
1.92-1.998.40.418470.99699.9
1.99-2.089.60.26219080.98100
2.08-2.19100.18518901.002100
2.19-2.3310.10.13719091.069100
2.33-2.5110.30.1119031.107100
2.51-2.7610.60.07619301.036100
2.76-3.1610.70.05319330.983100
3.16-3.9910.50.03819741.03299.9
3.99-509.60.0320961.13598.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.74 Å
Translation2.5 Å28.74 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→57.45 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2389 / WRfactor Rwork: 0.1925 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8402 / SU B: 6.262 / SU ML: 0.101 / SU R Cruickshank DPI: 0.1395 / SU Rfree: 0.1327 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 982 5.1 %RANDOM
Rwork0.1955 18154 --
obs0.1973 19136 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 37.23 Å2 / Biso mean: 34.204 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.33 Å20 Å2
2--0.65 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.85→57.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1454 0 54 123 1631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221568
X-RAY DIFFRACTIONr_angle_refined_deg2.4612.0052117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9315188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.00726.58582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69415301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.47152
X-RAY DIFFRACTIONr_chiral_restr0.3740.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021170
X-RAY DIFFRACTIONr_mcbond_it1.0631.5905
X-RAY DIFFRACTIONr_mcangle_it1.65621458
X-RAY DIFFRACTIONr_scbond_it2.9623663
X-RAY DIFFRACTIONr_scangle_it4.1584.5654
LS refinement shellResolution: 1.846→1.894 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 62 -
Rwork0.266 1202 -
all-1264 -
obs--92.8 %
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)
114.57322.3119-3.436435.89492.165911.03630.04370.1983-0.44520.06150.5273-2.1802-0.20541.665-0.5710.19210.0612-0.02430.3784-0.080.2411.426-9.5433-11.4779
210.4966-12.1811-3.895818.99793.17061.92060.219-0.20250.3631-0.3985-0.0354-0.4136-0.23580.1311-0.18360.32350.03580.00170.0819-0.00770.0586-5.51431.6537-8.3921
34.3374-0.5632-1.07725.71730.54198.26070.1466-0.40960.29010.04380.10910.1737-0.7929-0.1363-0.25570.25450.0927-0.0410.0875-0.04330.1112-12.203111.3826-10.1456
44.3903-1.9198-0.99062.4905-0.12123.49750.21250.0325-0.121-0.4241-0.10340.1662-0.3186-0.183-0.10910.3150.1418-0.08880.104-0.01720.1508-16.354711.101-20.8687
53.1477-3.03970.347.90112.46439.84530.122-0.1431-0.3782-0.1653-0.05080.6793-0.031-0.3535-0.07120.13940.0771-0.08190.08120.00750.1973-16.97041.5252-13.3068
610.4751-6.2056-8.7929.13847.028312.64330.08280.1636-0.409-2.2554-0.03130.0732-0.61410.4169-0.05151.04560.0684-0.03140.1696-0.00710.1852-7.3271-4.14-28.9372
77.6917-0.3088-3.680919.81382.583413.9421-0.1746-0.14890.0026-0.2720.0269-0.90290.24311.16430.14770.20330.0927-0.01850.21590.02510.14560.20693.8407-17.8632
83.90926.83692.900617.30015.73772.2350.38990.3427-0.1489-0.0903-0.2981-0.02120.20120.1457-0.09180.48850.2464-0.01890.2154-0.00950.0825-3.5104-8.4679-21.4501
94.3781-1.30421.49514.15040.96088.24320.51670.4287-0.6633-0.6583-0.29350.31390.6533-0.171-0.22320.41070.1657-0.19520.127-0.09390.2421-7.5447-19.2809-20.8583
105.69480.52063.31164.92810.41325.55340.3688-0.2955-0.8466-0.0854-0.03150.64350.8578-0.4953-0.33730.3148-0.0016-0.09730.1380.03990.35-13.2803-20.4962-10.9129
113.5845-1.2156-0.84344.24281.38418.36590.36090.3778-0.3605-0.6414-0.20450.45330.353-0.2752-0.15630.25880.1046-0.1990.1189-0.0420.2537-14.9797-11.5992-18.8276
1210.27947.595911.87016.27966.991119.8619-0.1388-0.68761.26060.0147-0.64731.32050.0803-0.49280.7860.15010.07150.12360.1628-0.08430.5367-10.6577-3.8271-1.8767
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 5
2X-RAY DIFFRACTION2A6 - 16
3X-RAY DIFFRACTION3A17 - 40
4X-RAY DIFFRACTION4A41 - 63
5X-RAY DIFFRACTION5A64 - 78
6X-RAY DIFFRACTION6A79 - 89
7X-RAY DIFFRACTION7B0 - 5
8X-RAY DIFFRACTION8B6 - 16
9X-RAY DIFFRACTION9B17 - 40
10X-RAY DIFFRACTION10B41 - 63
11X-RAY DIFFRACTION11B64 - 78
12X-RAY DIFFRACTION12B79 - 89

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