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- PDB-1j55: The Crystal Structure of Ca+-bound Human S100P Determined at 2.0A... -

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Basic information

Entry
Database: PDB / ID: 1j55
TitleThe Crystal Structure of Ca+-bound Human S100P Determined at 2.0A Resolution by X-ray
ComponentsS-100P PROTEIN
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


RAGE receptor binding / S100 protein binding / microvillus membrane / transition metal ion binding / endothelial cell migration / : / sarcoplasmic reticulum / calcium-dependent protein binding / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction ...RAGE receptor binding / S100 protein binding / microvillus membrane / transition metal ion binding / endothelial cell migration / : / sarcoplasmic reticulum / calcium-dependent protein binding / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / cadherin binding / calcium ion binding / positive regulation of cell population proliferation / Neutrophil degranulation / perinuclear region of cytoplasm / magnesium ion binding / protein homodimerization activity / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
S-100 / 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 / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. ...S-100 / 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 / Recoverin; domain 1 / EF-hand, calcium binding motif / 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 / Resolution: 2 Å
AuthorsZhang, H. / Wang, G. / Ding, Y. / Wang, Z. / Barraclough, R. / Rudland, P.S. / Fernig, D.G. / Rao, Z.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The Crystal Structure at 2A Resolution of the Ca2+-binding Protein S100P
Authors: Zhang, H. / Wang, G. / Ding, Y. / Wang, Z. / Barraclough, R. / Rudland, P.S. / Fernig, D.G. / Rao, Z.
History
DepositionJan 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: 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 / 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.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_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

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Assembly

Deposited unit
A: S-100P PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4923
Polymers10,4121
Non-polymers802
Water82946
1
A: S-100P PROTEIN
hetero molecules

A: S-100P PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9846
Polymers20,8242
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3210 Å2
ΔGint-79 kcal/mol
Surface area9630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.827, 60.827, 47.610
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein S-100P PROTEIN


Mass: 10411.884 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P25815
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.5
Details: PEG4000, sodium citrate, calcium chloride, pH 6.5, EVAPORATION, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mg/mlprotein1drop
230-34 %(w/v)PEG40001reservoir
30.1 Msodium citrate1reservoirpH6.5
40.5-2.0 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 11, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 57925 / Num. obs: 57916 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 14.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.403 / Num. unique all: 615 / % possible all: 96.6
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 6442 / % possible obs: 100 %
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 100 % / Num. unique obs: 615 / Mean I/σ(I) obs: 58.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementResolution: 2→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 680 -random
Rwork0.214 ---
all-6442 --
obs-6226 96.6 %-
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms673 0 2 46 721
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.68
Refinement
*PLUS
Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.225

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