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

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Basic information

Entry
Database: PDB / ID: 3czt
TitleCrystal Structure of S100B in the Calcium and Zinc Loaded State at pH 9
ComponentsProtein S100-B
KeywordsMETAL BINDING PROTEIN / S100 / EF-hand / Calcium / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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
DepositionApr 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
X: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9135
Polymers10,7271
Non-polymers1864
Water3,261181
1
X: Protein S100-B
hetero molecules

X: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,82510
Polymers21,4542
Non-polymers3718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area3310 Å2
ΔGint-165 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.980, 89.260, 59.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11X-94-

CA

21X-252-

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: 10727.037 Da / Num. of mol.: 1
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.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 43.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.02 M TAPS, pH 9.0, 30% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91853 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91853 Å / Relative weight: 1
ReflectionResolution: 1.4→17.8 Å / Num. obs: 18236 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.159 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.42
Reflection shellResolution: 1.4→1.55 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 5.1 / Num. measured obs: 14292 / Num. unique all: 4340 / Num. unique obs: 4340 / % possible all: 89.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.434 / Cor.coef. Fo:Fc: 0.408
Highest resolutionLowest resolution
Rotation4 Å28.92 Å
Translation4 Å28.92 Å

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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 1MHO

1mho


Resolution: 1.4→17.8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.678 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.222 911 5 %RANDOM
Rwork0.162 ---
obs0.164 18231 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.039 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→17.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms739 0 4 181 924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021804
X-RAY DIFFRACTIONr_bond_other_d0.0010.02540
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9491085
X-RAY DIFFRACTIONr_angle_other_deg1.31331339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.545104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.69926.73946
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59515162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.336151
X-RAY DIFFRACTIONr_chiral_restr0.1040.2115
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02920
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02153
X-RAY DIFFRACTIONr_mcbond_it1.7331.5480
X-RAY DIFFRACTIONr_mcbond_other0.7731.5195
X-RAY DIFFRACTIONr_mcangle_it2.432778
X-RAY DIFFRACTIONr_scbond_it4.0663324
X-RAY DIFFRACTIONr_scangle_it5.1994.5303
X-RAY DIFFRACTIONr_rigid_bond_restr2.4931344
X-RAY DIFFRACTIONr_sphericity_free8.4463185
X-RAY DIFFRACTIONr_sphericity_bonded4.01531325
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 52 -
Rwork0.218 989 -
all-1041 -
obs--100 %

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