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- PDB-3iqo: 1.5 angstrom X-ray structure of bovine Ca(2+)-S100B -

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Basic information

Entry
Database: PDB / ID: 3iqo
Title1.5 angstrom X-ray structure of bovine 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
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsCharpentier, T.H. / Weber, D.J. / Toth, E.A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: The Effects of CapZ Peptide (TRTK-12) Binding to S100B-Ca(2+) as Examined by NMR and X-ray Crystallography
Authors: Charpentier, T.H. / Thompson, L.E. / Liriano, M.A. / Varney, K.M. / Wilder, P.T. / Pozharski, E. / Toth, E.A. / Weber, D.J.
History
DepositionAug 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
B: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5246
Polymers21,3642
Non-polymers1604
Water2,576143
1
A: Protein S100-B
hetero molecules

A: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5246
Polymers21,3642
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2940 Å2
ΔGint-77 kcal/mol
Surface area9780 Å2
MethodPISA
2
B: Protein S100-B
hetero molecules

B: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5246
Polymers21,3642
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area2980 Å2
ΔGint-80 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.637, 35.044, 58.113
Angle α, β, γ (deg.)90.000, 92.620, 90.000
Int Tables number5
Space group name H-MC121

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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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 295 K / Method: sitting drop / pH: 6.3
Details: 25% PEG3350, 7.5mM CaCl2, 100mM Cacodylate buffer, pH 6.3, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→32.63 Å / Num. obs: 26110 / % possible obs: 89.4 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.061 / Χ2: 1.09 / Net I/σ(I): 20.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.551.50.24720971.04172.7
1.55-1.621.80.2425051.079185.8
1.62-1.692.10.22326981.07193.9
1.69-1.782.40.17728511.084198.1
1.78-1.892.80.15628491.336198.5
1.89-2.043.10.12428641.102198.4
2.04-2.243.20.08828371.03197.2
2.24-2.563.10.06327581.07194.1
2.56-3.232.90.04726891.051191.1
3.23-502.50.0419620.934164.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.63 Å
Translation2.5 Å32.63 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
Starting model: PDB entry 1MHO

1mho


Resolution: 1.5→32.63 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.314 / WRfactor Rwork: 0.269 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.764 / SU B: 4.61 / SU ML: 0.084 / SU R Cruickshank DPI: 0.111 / SU Rfree: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1323 5.1 %RANDOM
Rwork0.2 ---
obs0.202 26069 89.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.71 Å2 / Biso mean: 32.557 Å2 / Biso min: 21.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20.08 Å2
2--0.65 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.5→32.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1420 0 4 143 1567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221479
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.9541993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3385186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.98126.4178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45215291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.563152
X-RAY DIFFRACTIONr_chiral_restr0.0990.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021104
X-RAY DIFFRACTIONr_nbd_refined0.2210.2713
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21027
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2104
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.230
X-RAY DIFFRACTIONr_mcbond_it0.8171.5910
X-RAY DIFFRACTIONr_mcangle_it1.21621443
X-RAY DIFFRACTIONr_scbond_it2.3913612
X-RAY DIFFRACTIONr_scangle_it3.8074.5543
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 67 -
Rwork0.238 1408 -
all-1475 -
obs--68.38 %
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)
141.8999.623110.817319.01469.241420.86190.3395-0.4385-1.99760.7207-0.0047-0.48750.878-0.0043-0.3348-0.1337-0.00020.0065-0.16580.0118-0.07785.5757-3.764-2.6539
238.3192-11.12886.42526.9542-2.39472.1126-0.0270.9913-0.2666-0.3484-0.05920.20760.2154-0.14240.0861-0.1389-0.04450.014-0.06-0.0312-0.2115-5.59640.8379-6.7966
34.8520.09050.69274.8436-2.99459.6619-0.04720.52930.0123-0.21750.13850.2620.0037-0.1943-0.0913-0.1743-0.0218-0.0098-0.12770.0079-0.18-16.45844.7316-4.9139
45.7602-3.4291.09816.1429-2.32993.5205-0.2217-0.31730.34830.32830.1887-0.033-0.145-0.1110.033-0.10660.0024-0.0286-0.1311-0.0194-0.0937-17.124110.12295.3163
511.5837-1.48558.32255.2742-3.073715.8260.11170.70570.285-0.23360.06150.1815-0.13320.2318-0.1732-0.1546-0.0138-0.0015-0.14660.0411-0.1099-8.525811.8899-3.7343
614.2059-2.67768.614130.4046-5.841333.0265-0.3401-1.3651-0.45843.36230.431-0.4085-0.10690.3066-0.0910.21920.0491-0.0190.03580.011-0.1213-1.45946.622312.1704
743.8215-5.263-2.812223.1698-2.408212.80830.203-0.5543.1153-0.1218-0.29630.602-0.49330.40150.0933-0.1851-0.0149-0.0321-0.1358-0.09120.18677.27722.4573-26.0885
839.84775.6882-5.104510.21680.56340.8314-0.2036-1.25331.03480.7090.2089-0.2216-0.0630.0494-0.0053-0.12040.0359-0.0231-0.0507-0.0764-0.1175-4.2941-2.0752-22.2581
93.981-0.4105-0.05216.1969-3.532511.46740.0083-0.31430.00570.30010.13030.3402-0.0362-0.3487-0.1386-0.17390.00790.0219-0.13410.0034-0.1695-15.1842-5.9107-24.1402
104.69163.409-0.90125.9467-1.26122.5097-0.05140.3455-0.1891-0.34860.0607-0.02820.0817-0.1088-0.0092-0.12170.0165-0.0004-0.0974-0.0075-0.0965-15.8085-11.3926-34.313
118.70490.543-6.67457.5883-2.675312.17540.0702-0.3788-0.25860.38820.01950.2241-0.00340.1561-0.0896-0.15370.01090.0008-0.16510.0394-0.1366-7.2887-13.1308-25.2107
129.3801-1.0022-6.66027.3191-10.740531.4205-0.16530.5917-0.0619-0.6648-0.2238-0.0060.37150.13210.3891-0.0406-0.00310.0015-0.09740.0049-0.15630.2168-8.0218-41.0376
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 DIFFRACTION7B1 - 5
8X-RAY DIFFRACTION8B6 - 16
9X-RAY DIFFRACTION9B17 - 40
10X-RAY DIFFRACTION10B41 - 63
11X-RAY DIFFRACTION11B64 - 78
12X-RAY DIFFRACTION12B79 - 88

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