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- PDB-3psr: HUMAN PSORIASIN (S100A7) CA2+ BOUND FORM (CRYSTAL FORM I) -

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Basic information

Entry
Database: PDB / ID: 3psr
TitleHUMAN PSORIASIN (S100A7) CA2+ BOUND FORM (CRYSTAL FORM I)
ComponentsPSORIASIN
KeywordsEF-HAND PROTEIN / CA-BINDING / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBrodersen, D.E. / Nyborg, J. / Kjeldgaard, M.
Citation
Journal: Biochemistry / Year: 1999
Title: Zinc-binding site of an S100 protein revealed. Two crystal structures of Ca2+-bound human psoriasin (S100A7) in the Zn2+-loaded and Zn2+-free states.
Authors: Brodersen, D.E. / Nyborg, J. / Kjeldgaard, M.
#1: 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.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Psoriasin
Authors: Nolsoe, S. / Thirup, S. / Etzerodt, M. / Thogersen, H.C. / Nyborg, J.
#3: 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
DepositionSep 17, 1998Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)22,8335
Polymers22,6882
Non-polymers1463
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-59 kcal/mol
Surface area10210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.150, 56.670, 76.380
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: (0.1597, 0.9314, 0.3272), (0.9269, -0.2556, 0.275), (0.3397, 0.2593, -0.9041)
Vector: -17.5848, 8.4814, 38.3392)

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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: CHAIN A IS CA2+ AND ZN2+ BOUND FORM, CHAIN B IS CA2+ BOUND FORM
Source: (gene. exp.) Homo sapiens (human) / Cell: 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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.: 70 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFOR THIS STRUCTURE, ONLY ONE OF THE TWO ZINC BINDING SITES ACTUALLY BINDS ZINC (MONOMER A), WHEREAS ...FOR THIS STRUCTURE, ONLY ONE OF THE TWO ZINC BINDING SITES ACTUALLY BINDS ZINC (MONOMER A), WHEREAS THE OTHER (MONOMER B) DOES NOT. ONLY ONE ZINC SITE IS LISTED ON SITE RECORDS BELOW.
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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growpH: 7.7 / Details: pH 7.7
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: unknown / PH range low: 8 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15.5 mg/mlprotein11
222 %(w/v)PEG400011
35-10 %(v/v)glycerol11
45-10 mM11CaCl2

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→34.3 Å / Num. obs: 8199 / % possible obs: 99.3 % / Redundancy: 5.4 % / Rsym value: 0.122 / Net I/σ(I): 5.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.544 / % possible all: 99.3
Reflection
*PLUS
Rmerge(I) obs: 0.122
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.544

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
SHELXL-97model building
SHELXL-97refinement
CCP4(SCALA)data scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PSR

1psr


Resolution: 2.5→100 Å / Num. parameters: 6450 / Num. restraintsaints: 8061 / Cross valid method: FREE R / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2953 415 5.1 %RANDOM
all0.223 8172 --
obs0.2199 -52 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91(1973) 201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1610.3
Refinement stepCycle: LAST / Resolution: 2.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 0 3 70 1611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.015
X-RAY DIFFRACTIONs_similar_dist0.038
X-RAY DIFFRACTIONs_from_restr_planes0.245
X-RAY DIFFRACTIONs_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.024
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.066
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.224 / Rfactor Rfree: 0.293
Solvent computation
*PLUS
Displacement parameters
*PLUS

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