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- PDB-4fqo: Crystal Structure of Calcium-Loaded S100B Bound to SBi4211 -

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Basic information

Entry
Database: PDB / ID: 4fqo
TitleCrystal Structure of Calcium-Loaded S100B Bound to SBi4211
ComponentsProtein S100-B
Keywordsprotein binding/inhibitor / protein-inhibitor complex / EF-hand protein / Calcium binding protein / protein binding-inhibitor complex
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 / sarcoplasmic reticulum / 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 / perinuclear region of cytoplasm / 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-AZ3 / Protein S100-B
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsMcKnight, L.E. / Raman, E.P. / Bezawada, P. / Kudrimoti, S. / Wilder, P.T. / Hartman, K.G. / Toth, E.A. / Coop, A. / MacKerrell, A.D. / Weber, D.J.
CitationJournal: ACS Med Chem Lett / Year: 2012
Title: Structure-Based Discovery of a Novel Pentamidine-Related Inhibitor of the Calcium-Binding Protein S100B.
Authors: McKnight, L.E. / Raman, E.P. / Bezawada, P. / Kudrimoti, S. / Wilder, P.T. / Hartman, K.G. / Godoy-Ruiz, R. / Toth, E.A. / Coop, A. / Mackerell, A.D. / Weber, D.J.
History
DepositionJun 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 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 / pdbx_struct_special_symmetry / 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
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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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)10,7344
Polymers10,2861
Non-polymers4493
Water1,60389
1
A: Protein S100-B
hetero molecules

A: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4688
Polymers20,5712
Non-polymers8976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3130 Å2
ΔGint-82 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.079, 63.079, 48.998
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-103-

AZ3

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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: 10285.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02638
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Details: Synthesized according to previously published protocols
#3: Chemical ChemComp-AZ3 / 4,4'-[heptane-1,7-diylbis(oxy)]dibenzenecarboximidamide


Mass: 368.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.21
Details: PEG3350, sodium cacodylate, calcium chloride, pH 7.21, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 12333 / % possible obs: 99.6 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.068 / Χ2: 1.043 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.6813.50.6515951.0051100
1.68-1.7113.60.5416081.0091100
1.71-1.7413.90.4885991.0471100
1.74-1.7813.80.4166061.0911100
1.78-1.8213.90.3266141.0861100
1.82-1.8613.90.2735971.0811100
1.86-1.913.90.2526061.0921100
1.9-1.9613.90.196071.0511100
1.96-2.0113.90.1486081.0551100
2.01-2.0813.80.136071.0631100
2.08-2.1513.90.1166161.0351100
2.15-2.2413.80.1036131.0271100
2.24-2.3413.70.0966150.9831100
2.34-2.4613.70.096091.0631100
2.46-2.6213.50.0876261.0411100
2.62-2.8213.50.0756230.9971100
2.82-3.1113.30.0636240.9521100
3.11-3.5513.10.0546441.0661100
3.55-4.4813.20.0536561.0691100
4.48-5011.30.0586601.053192.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.5.0102refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→44.6 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.353 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 590 4.8 %RANDOM
Rwork0.1988 ---
obs0.1995 12291 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 231.24 Å2 / Biso mean: 34.349 Å2 / Biso min: 15.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2---0.54 Å2-0 Å2
3---1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms712 0 29 89 830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022767
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9961027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.261594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46426.57938
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.715150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.469151
X-RAY DIFFRACTIONr_chiral_restr0.1020.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02571
X-RAY DIFFRACTIONr_mcbond_it0.8731.5449
X-RAY DIFFRACTIONr_mcangle_it1.5262723
X-RAY DIFFRACTIONr_scbond_it2.4443318
X-RAY DIFFRACTIONr_scangle_it4.0054.5301
LS refinement shellResolution: 1.652→1.695 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 48 -
Rwork0.213 832 -
all-880 -
obs--99.89 %
Refinement TLS params.Method: refined / Origin x: 13.9566 Å / Origin y: 1.0265 Å / Origin z: 9.6102 Å
111213212223313233
T0.0811 Å20.0023 Å2-0.0222 Å2-0.0415 Å20.0291 Å2--0.0662 Å2
L3.8548 °20.3375 °2-1.618 °2-2.0414 °2-0.2767 °2--2.3793 °2
S0.0696 Å °-0.038 Å °0.221 Å °0.1986 Å °-0.0533 Å °-0.2576 Å °-0.1904 Å °0.0698 Å °-0.0163 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 88
2X-RAY DIFFRACTION1A101 - 102
3X-RAY DIFFRACTION1A103
4X-RAY DIFFRACTION1A201 - 289

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