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- PDB-1psr: HUMAN PSORIASIN (S100A7) -

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Basic information

Entry
Database: PDB / ID: 1psr
TitleHUMAN PSORIASIN (S100A7)
ComponentsPSORIASIN
KeywordsEF-HAND PROTEIN / MAD PHASING / PSORIASIS / S100 PROTEIN FAMILY
Function / homology
Function and homology information


zinc ion sequestering activity / positive regulation of granulocyte chemotaxis / Metal sequestration by antimicrobial proteins / positive regulation of T cell chemotaxis / RAGE receptor binding / positive regulation of monocyte chemotaxis / epidermis development / endothelial cell migration / keratinocyte differentiation / response to reactive oxygen species ...zinc ion sequestering activity / positive regulation of granulocyte chemotaxis / Metal sequestration by antimicrobial proteins / positive regulation of T cell chemotaxis / RAGE receptor binding / positive regulation of monocyte chemotaxis / epidermis development / endothelial cell migration / keratinocyte differentiation / response to reactive oxygen species / antimicrobial humoral immune response mediated by antimicrobial peptide / calcium-dependent protein binding / azurophil granule lumen / : / angiogenesis / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / focal adhesion / calcium ion binding / Neutrophil degranulation / endoplasmic reticulum / extracellular space / extracellular region / zinc ion binding / nucleus / cytosol / 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 1, calcium-binding site / EF-hand calcium-binding domain. ...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 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
HOLMIUM ATOM / Protein S100-A7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MULTI-WAVELENGTH ANOMALOUS DISPERSION / Resolution: 1.05 Å
AuthorsBrodersen, D.E. / Etzerodt, M. / Madsen, P. / Celis, J. / Thoegersen, H.C. / Nyborg, J. / Kjeldgaard, M.
Citation
Journal: Structure / Year: 1998
Title: EF-hands at atomic resolution: the structure of human psoriasin (S100A7) solved by MAD phasing.
Authors: Brodersen, D.E. / Etzerodt, M. / Madsen, P. / Celis, J.E. / Thogersen, H.C. / Nyborg, J. / Kjeldgaard, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Psoriasin
Authors: Nolsoe, S. / Thirup, S. / Etzerodt, M. / Thoegersen, H.C. / Nyborg, J.
#2: Journal: J.Invest.Dermatol. / Year: 1991
Title: Molecular Cloning, Occurrence, and Expression of a Novel Partially Secreted Protein "Psoriasin" that is Highly Up-Regulated in Psoriatic Skin
Authors: Madsen, P. / Rasmussen, H.H. / Leffers, H. / Honore, B. / Dejgaard, K. / Olsen, E. / Kiil, J. / Walbum, E. / Andersen, A.H. / Basse, B. / Lauridsen, J.B. / Ratz, G.P. / Celis, A. / ...Authors: Madsen, P. / Rasmussen, H.H. / Leffers, H. / Honore, B. / Dejgaard, K. / Olsen, E. / Kiil, J. / Walbum, E. / Andersen, A.H. / Basse, B. / Lauridsen, J.B. / Ratz, G.P. / Celis, A. / Vandekerckhove, J. / Celis, J.E.
History
DepositionNov 27, 1997Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / 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 / _diffrn_source.pdbx_synchrotron_site / _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_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_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: PSORIASIN
B: PSORIASIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0174
Polymers22,6882
Non-polymers3302
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-39 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.805, 61.631, 62.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.7741, 0.413, -0.4797), (0.413, -0.2448, -0.8772), (-0.4797, -0.8772, 0.0189)
Vector: 23.0275, 72.786, 73.5038)

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Components

#1: Protein PSORIASIN / S100A7


Mass: 11343.784 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CA2+ SUBSTITUTED FOR HO3+ / Source: (gene. exp.) Homo sapiens (human) / Tissue: KERATINOCYTES
Cellular location: CYTOPLASMIC OR MAY BE SECRETED BY A NON-CLASSICAL SECRETORY PATHWAY
Plasmid: PT7H6FX-PS.4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P31151
#2: Chemical ChemComp-HO / HOLMIUM ATOM


Mass: 164.930 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ho
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 39 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / PH range low: 7.5 / PH range high: 4.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18.6 mg/mlprotein1drop
220-30 %(w/v)PEGmmes 20001reservoir
350-300 mMammonium sulfate1reservoir
4100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9091
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 1997 / Details: SEGMENTED MIRROR
RadiationMonochromator: BENT SINGLE-CRYSTAL GERMANIUM TRIANGULAR MONOCHROMATOR
Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9091 Å / Relative weight: 1
ReflectionResolution: 1.05→37.5 Å / Num. obs: 160437 / % possible obs: 97.9 % / Redundancy: 1.8 % / Rsym value: 0.033 / Net I/σ(I): 28.7
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 1.18 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.103 / % possible all: 84.1
Reflection
*PLUS
Num. obs: 84591 / Num. measured all: 700858 / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 84.1 % / Rmerge(I) obs: 0.101

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97model building
SHELXL-97refinement
SHELXL-97phasing
RefinementMethod to determine structure: MULTI-WAVELENGTH ANOMALOUS DISPERSION
Highest resolution: 1.05 Å / Num. parameters: 18753 / Num. restraintsaints: 19286 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1412 2545 3.1 %RANDOM
all0.1087 82046 --
obs0.1072 -96.3 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. (1973) 91: 201-228
Refine analyzeNum. disordered residues: 19 / Occupancy sum hydrogen: 1394.2 / Occupancy sum non hydrogen: 1925.6
Refinement stepCycle: LAST / Highest resolution: 1.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1586 0 2 387 1975
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.03
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.105
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.099
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.056
X-RAY DIFFRACTIONs_approx_iso_adps0.016
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 37.5 Å / Num. reflection obs: 160437 / Rfactor obs: 0.1049 / Rfactor Rwork: 0.1072
Solvent computation
*PLUS
Displacement parameters
*PLUS

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