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- PDB-3d10: Crystal Structure of S100B in the Calcium and Zinc Loaded State a... -

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Basic information

Entry
Database: PDB / ID: 3d10
TitleCrystal Structure of S100B in the Calcium and Zinc Loaded State at pH 10.0
ComponentsProtein S100-B
KeywordsMETAL BINDING PROTEIN / S100B / S100 / EF-hand / Metal-binding / Nucleus
Function / homology
Function and homology information


adaptive thermogenesis / sympathetic neuron projection extension / RAGE receptor binding / S100 protein binding / regulation of neuronal synaptic plasticity / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / Nuclear signaling by ERBB4 / ruffle / positive regulation of neuron differentiation ...adaptive thermogenesis / sympathetic neuron projection extension / RAGE receptor binding / S100 protein binding / regulation of neuronal synaptic plasticity / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / Nuclear signaling by ERBB4 / ruffle / positive regulation of neuron differentiation / axonogenesis / central nervous system development / TAK1-dependent IKK and NF-kappa-B activation / tau protein binding / memory / calcium-dependent protein binding / positive regulation of canonical NF-kappaB signal transduction / learning or memory / cell adhesion / intracellular membrane-bounded organelle / neuronal cell body / positive regulation of cell population proliferation / calcium ion binding / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / 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
TRIETHYLENE GLYCOL / Protein S100-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsOstendorp, T. / Diez, J. / Heizmann, C.W. / Fritz, G.
CitationJournal: Biochim.Biophys.Acta / Year: 2011
Title: The crystal structures of human S100B in the zinc- and calcium-loaded state at three pH values reveal zinc ligand swapping.
Authors: Ostendorp, T. / Diez, J. / Heizmann, C.W. / Fritz, G.
History
DepositionMay 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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_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.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_conn.ptnr2_label_seq_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)21,8959
Polymers21,4542
Non-polymers4417
Water2,738152
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-158 kcal/mol
Surface area10120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.750, 58.180, 47.850
Angle α, β, γ (deg.)90.000, 111.080, 90.000
Int Tables number4
Space group name H-MP1211

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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: 10727.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100B / Plasmid: pGEMEX-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04271
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 10
Details: 0.02 M CAPS pH 10.0, 23% PEG5000MME, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0089 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0089 Å / Relative weight: 1
ReflectionResolution: 1.55→10 Å / Num. obs: 25152 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 31.619 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 5.34
Reflection shellResolution: 1.55→1.6 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2 / Num. measured obs: 5373 / Num. unique obs: 2236 / % possible all: 95.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2H61 chain A and B

2h61


Resolution: 1.65→10 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.627 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1058 5.1 %RANDOM
Rwork0.209 ---
obs0.212 20791 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.549 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20 Å2-0.4 Å2
2--0.39 Å20 Å2
3----2.06 Å2
Refinement stepCycle: LAST / Resolution: 1.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 16 152 1656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211534
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.9522050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3715185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06926.47185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43315300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.505152
X-RAY DIFFRACTIONr_chiral_restr0.1510.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021152
X-RAY DIFFRACTIONr_nbd_refined0.2460.2829
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21048
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2114
X-RAY DIFFRACTIONr_metal_ion_refined0.1770.220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.228
X-RAY DIFFRACTIONr_mcbond_it1.3251.5955
X-RAY DIFFRACTIONr_mcangle_it1.70821469
X-RAY DIFFRACTIONr_scbond_it2.8733642
X-RAY DIFFRACTIONr_scangle_it4.0124.5580
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 64 -
Rwork0.247 1456 -
all-1520 -
obs--98.13 %
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)
13.5060.13470.95261.3062-0.54083.7077-0.0327-0.64340.12320.2013-0.09020.1279-0.1913-0.18250.12290.02130.03160.04760.0611-0.03310.16453.49091.306311.2172
22.8771.45411.30199.6249-3.61178.0327-0.03090.1136-0.07770.04390.0166-0.08790.04690.25550.01430.00440.0186-0.01490.1605-0.04920.132314.8559-4.278118.8157
33.77034.09851.197811.75094.95136.6904-0.0956-0.2749-0.4316-0.10760.1228-0.12490.39730.1502-0.02720.02350.0146-0.00240.03230.04020.229.8553-8.18534.4109
47.3622-0.9621-4.18944.67210.451534.19550.0774-0.2335-0.0793-0.0363-0.4770.38990.5034-1.25120.39970.2099-0.04560.00190.00190.01390.34310.2938-7.4914-0.5663
54.0894-0.9737-1.39032.97470.41396.23080.08770.3216-0.1056-0.2321-0.0523-0.08930.30460.4635-0.03540.04740.0473-0.00830.0826-0.02640.12848.9521-2.3873-15.9526
64.4574-4.4098-0.995916.49527.48948.7640.16710.17960.29940.235-0.358-0.0908-0.03670.15750.19090.045700.0140.080.02450.19589.48953.2555-3.6774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 451 - 46
2X-RAY DIFFRACTION2AA46 - 6647 - 67
3X-RAY DIFFRACTION3AA67 - 9168 - 92
4X-RAY DIFFRACTION4BB0 - 161 - 17
5X-RAY DIFFRACTION5BB17 - 6618 - 67
6X-RAY DIFFRACTION6BB67 - 9068 - 91

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