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- PDB-3rlz: 2.0 Angstrom X-ray structure of bovine Ca(2+)-S100B D63N -

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Basic information

Entry
Database: PDB / ID: 3rlz
Title2.0 Angstrom X-ray structure of bovine Ca(2+)-S100B D63N
ComponentsProtein S100-B
KeywordsMETAL BINDING PROTEIN / alpha-helical / EF hand
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 / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsLiriano, M.A. / Weber, D.J.
CitationJournal: To be Published
Title: The effects of CapZ peptide (TRTK12) on the protein dynamics of S100B and S100B D63N
Authors: Liriano, M.A. / Varney, K.M. / Inman, K.G. / Ishima, R. / Weber, D.J.
History
DepositionApr 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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_ref_seq_dif.details / _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)21,5226
Polymers21,3622
Non-polymers1604
Water1,49583
1
A: Protein S100-B
hetero molecules

A: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5226
Polymers21,3622
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2900 Å2
ΔGint-59 kcal/mol
Surface area9500 Å2
MethodPISA
2
B: Protein S100-B
hetero molecules

B: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5226
Polymers21,3622
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3050 Å2
ΔGint-78 kcal/mol
Surface area9680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.823, 34.950, 57.584
Angle α, β, γ (deg.)90.000, 92.800, 90.000
Int Tables number5
Space group name H-MC121

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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: 10680.989 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.: 83 / 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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 295 K / Method: sitting drop / pH: 7
Details: 25% PEG3350, 7.5 mM calcium chloride, 100 mM cacodylate, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.01→57.52 Å / Num. obs: 11828 / % possible obs: 97.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.079 / Χ2: 1.878 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.01-2.083.20.30310861.07190.3
2.08-2.173.40.24211551.115195.5
2.17-2.263.50.17711501.504197.6
2.26-2.383.50.16211821.606197
2.38-2.533.60.13411712.314197.4
2.53-2.733.60.12511922.466198.5
2.73-33.60.11111973.369198.9
3-3.443.60.08912102.466199.5
3.44-4.333.50.05912231.39199.6
4.33-503.40.06112621.166199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IQQ

3iqq


Resolution: 2.01→57.52 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.637 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2587 565 4.8 %RANDOM
Rwork0.2079 ---
obs0.2103 11828 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.7 Å2 / Biso mean: 34.979 Å2 / Biso min: 3.97 Å2
Baniso -1Baniso -2Baniso -3
1--2.39 Å20 Å20.68 Å2
2--1.11 Å2-0 Å2
3---1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.01→57.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 4 83 1517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221448
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.951935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3595178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.10926.35174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48815278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.626152
X-RAY DIFFRACTIONr_chiral_restr0.1220.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021071
X-RAY DIFFRACTIONr_mcbond_it0.8581.5890
X-RAY DIFFRACTIONr_mcangle_it1.59521427
X-RAY DIFFRACTIONr_scbond_it2.5183558
X-RAY DIFFRACTIONr_scangle_it3.9984.5508
LS refinement shellResolution: 2.011→2.063 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.483 25 -
Rwork0.269 751 -
all-776 -
obs--89.5 %
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)
10.88410.2186-2.94720.83571.415115.7117-0.0080.0771-0.03370.07240.1771-0.10550.27130.1518-0.1690.0460.02930.00880.11280.05610.2572-6.72419.458514.8791
20.07340.1613-0.13230.3716-0.29730.2443-0.0140.0192-0.0307-0.0529-0.0328-0.080.0507-0.02920.04690.26910.00510.00520.40640.0310.28544.96599.334714.4828
30.02370.06640.03950.5881-0.39940.93270.0017-0.00240.02450.0013-0.0426-0.05140.0560.08990.04090.11790.00290.00040.1934-0.01530.172615.93879.377914.2049
40.780.1947-0.01760.7597-0.24480.5408-0.0257-0.01690.0353-0.01980.0058-0.0631-0.041-0.0120.01990.07450.01550.00810.0465-0.04980.157316.41739.155213.4551
50.03190.1372-0.1872.0154-1.74962.4884-0.0190.00730.03580.00950.0574-0.0506-0.0129-0.0332-0.03840.0526-0.0029-0.00020.1286-0.03040.21367.80289.616314.1089
60.28470.3435-0.53022.2786-3.21910.75670.0623-0.0121-0.03490.01190.01140.06890.0021-0.0723-0.07370.01730.0145-0.01360.1594-0.02430.2253-0.40999.273114.575
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION1B1 - 5
3X-RAY DIFFRACTION2A6 - 16
4X-RAY DIFFRACTION2B6 - 16
5X-RAY DIFFRACTION3A17 - 40
6X-RAY DIFFRACTION3B17 - 40
7X-RAY DIFFRACTION4A41 - 63
8X-RAY DIFFRACTION4B41 - 63
9X-RAY DIFFRACTION5A64 - 78
10X-RAY DIFFRACTION5B64 - 78
11X-RAY DIFFRACTION6A79 - 89
12X-RAY DIFFRACTION6B79 - 89

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