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- PDB-2psr: HUMAN PSORIASIN (S100A7) CA2+ AND ZN2+ BOUND FORM (CRYSTAL FORM II) -

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Basic information

Entry
Database: PDB / ID: 2psr
TitleHUMAN PSORIASIN (S100A7) CA2+ AND ZN2+ BOUND FORM (CRYSTAL FORM II)
ComponentsPSORIASIN
KeywordsEF-HAND PROTEIN / CA-BINDING / ZN-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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PSORIASIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4493
Polymers11,3441
Non-polymers1052
Water1,910106
1
A: PSORIASIN
hetero molecules

A: PSORIASIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8996
Polymers22,6882
Non-polymers2114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2820 Å2
ΔGint-117 kcal/mol
Surface area10020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)51.958, 51.958, 116.027
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PSORIASIN / S100A7


Mass: 11343.784 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CA2+ AND ZN2+ 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.: 1 / 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.: 106 / 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: 3.06 Å3/Da / Density % sol: 59.7 %
Crystal growpH: 6.7 / Details: pH 6.7
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown / Details: or 20 degrees centigrade
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein11
25-12 %(v/v)PEG400011
310 %(v/v)glycerol11
420 mM11ZnSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.862
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.862 Å / Relative weight: 1
ReflectionResolution: 2.05→20.1 Å / Num. obs: 10791 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rsym value: 0.113 / Net I/σ(I): 15.9
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 5 / Rsym value: 0.423 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.113
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.423

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PSR

1psr


Resolution: 2.05→100 Å / Num. parameters: 3513 / Num. restraintsaints: 3122 / Cross valid method: FREE R / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 541 5 %RANDOM
all0.2165 10777 --
obs0.2146 -100 %-
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: 876.89
Refinement stepCycle: LAST / Resolution: 2.05→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms769 0 2 106 877
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.019
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.313
X-RAY DIFFRACTIONs_zero_chiral_vol0.027
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.034
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.006
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.077
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 10236 / Rfactor all: 0.219 / Rfactor obs: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS

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