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- PDB-3lk1: X-ray structure of bovine SC0322,Ca(2+)-S100B -

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Basic information

Entry
Database: PDB / ID: 3lk1
TitleX-ray structure of bovine SC0322,Ca(2+)-S100B
ComponentsProtein S100-B
KeywordsMETAL BINDING PROTEIN / EF hand / Alpha helical / Metal-binding
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
ETHYL MERCURY ION / 2-sulfanylbenzoic acid / Protein S100-B
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 26, 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
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)10,8795
Polymers10,4151
Non-polymers4644
Water84747
1
A: Protein S100-B
hetero molecules

A: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,75710
Polymers20,8292
Non-polymers9288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2640 Å2
ΔGint-29 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.194, 88.792, 58.996
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-138-

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: 10414.713 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-EMC / ETHYL MERCURY ION / Ethylmercury


Mass: 229.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5Hg
#4: Chemical ChemComp-JKE / 2-sulfanylbenzoic acid / Thiosalicylic acid


Mass: 154.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: PEGMME550, CaCl2, MgCl2, SC0322, HEPES buffer, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97607 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97607 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 7607 / % possible obs: 84.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.057 / Χ2: 1.22 / Net I/σ(I): 16.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.863.40.3082970.85333.4
1.86-1.943.80.274770.8754.8
1.94-2.034.30.2446741.04876.4
2.03-2.135.10.2017851.19189.5
2.13-2.275.80.1518591.33396.8
2.27-2.446.50.138901.33999.9
2.44-2.696.90.1029051.17399.9
2.69-3.086.80.0788881.18799.9
3.08-3.886.50.0539211.28199.9
3.88-506.40.0449111.27593.3

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Phasing

Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.5 Å
Translation2.5 Å29.5 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→29.5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.277 / WRfactor Rwork: 0.231 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.833 / SU B: 6.64 / SU ML: 0.106 / SU R Cruickshank DPI: 0.174 / SU Rfree: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 364 4.8 %RANDOM
Rwork0.196 ---
obs0.198 7593 84.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 447.11 Å2 / Biso mean: 49.817 Å2 / Biso min: 37.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---2.44 Å20 Å2
3---2.77 Å2
Refinement stepCycle: LAST / Resolution: 1.79→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms694 0 15 47 756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021716
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.965958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.772587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55726.38936
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21115133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.691151
X-RAY DIFFRACTIONr_chiral_restr0.1080.2106
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02535
X-RAY DIFFRACTIONr_nbd_refined0.2230.2334
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2495
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.238
X-RAY DIFFRACTIONr_metal_ion_refined0.1870.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.26
X-RAY DIFFRACTIONr_mcbond_it0.5581.5451
X-RAY DIFFRACTIONr_mcangle_it0.8062697
X-RAY DIFFRACTIONr_scbond_it1.4973295
X-RAY DIFFRACTIONr_scangle_it2.2854.5261
LS refinement shellResolution: 1.79→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 12 -
Rwork0.236 188 -
all-200 -
obs--30.4 %
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)
110.4199-7.07137.129363.1761-4.196124.2491-0.1393-0.13350.8244-1.22590.5578-1.81710.65081.1627-0.4185-0.1546-0.0056-0.0391-0.1674-0.01220.10363.175-5.89182.5575
23.1629-12.6881-2.872752.58812.88783.7101-0.1815-0.4643-0.28210.81670.5415-0.5451-0.07120.5447-0.36-0.0171-0.0202-0.0876-0.13490.0181-0.0641-1.66325.45076.5898
37.30570.0507-2.84565.70840.16558.4656-0.1109-0.44580.24070.5760.0029-0.1921-0.4530.07610.108-0.1338-0.0141-0.0194-0.2019-0.0134-0.1562-5.562216.29054.8908
47.0948-1.256-2.21386.45060.0155.37080.03890.239-0.0567-0.4155-0.11760.4114-0.1392-0.05650.0787-0.1452-0.0151-0.0226-0.182-0.0242-0.1397-10.982416.9433-5.1511
56.0901-2.6569-2.967113.66234.37558.5956-0.1949-0.3747-0.30420.7250.26160.71560.08590.0913-0.0667-0.1642-0.02080.0735-0.19230.04430.0041-12.66188.38373.437
625.38156.3681-18.79784.2671.820229.9287-1.25372.004-0.6077-1.79780.8577-0.03820.8231-1.02680.3960.267-0.17810.03930.02950.02070.1874-8.07561.9937-11.7932
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 - 87

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