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- PDB-4zk0: Psoriasis pathogenesis - Pso p27 constitute a compact structure f... -

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Basic information

Entry
Database: PDB / ID: 4zk0
TitlePsoriasis pathogenesis - Pso p27 constitute a compact structure forming large aggregates. High pH structure
ComponentsSerpin B4
KeywordsIMMUNE SYSTEM / hydrolase inhibitor / Autoimmunity / pathogenesis / Pso p27 / Pso p27-complex / psoriasis / SCCA1 / SerpinB3
Function / homology
Function and homology information


negative regulation of peptidase activity / autocrine signaling / positive regulation of endopeptidase activity / negative regulation of catalytic activity / negative regulation of endopeptidase activity / negative regulation of JUN kinase activity / paracrine signaling / cysteine-type endopeptidase inhibitor activity / positive regulation of epithelial to mesenchymal transition / negative regulation of proteolysis ...negative regulation of peptidase activity / autocrine signaling / positive regulation of endopeptidase activity / negative regulation of catalytic activity / negative regulation of endopeptidase activity / negative regulation of JUN kinase activity / paracrine signaling / cysteine-type endopeptidase inhibitor activity / positive regulation of epithelial to mesenchymal transition / negative regulation of proteolysis / serine-type endopeptidase inhibitor activity / azurophil granule lumen / virus receptor activity / protease binding / cytoplasmic vesicle / vesicle / positive regulation of cell migration / positive regulation of cell population proliferation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHelland, R. / Lysvand, H. / Slupphaug, G. / Iversen, O.J.
CitationJournal: Biochem Biophys Rep / Year: 2015
Title: Psoriasis pathogenesis - Pso p27 constitutes a compact structure forming large aggregates.
Authors: Lysvand, H. / Helland, R. / Hagen, L. / Slupphaug, G. / Iversen, O.J.
History
DepositionApr 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serpin B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7513
Polymers44,6201
Non-polymers1312
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-51 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.808, 68.273, 105.773
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serpin B4 / Leupin / Peptidase inhibitor 11 / PI-11 / Squamous cell carcinoma antigen 2 / SCCA-2


Mass: 44620.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINB4, PI11, SCCA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: P29508
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 22% PEGMME 5K, 0.1 M Bicine pH 8.5, 0.06 M Zn acetate, 4.5% Hexanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.15→57.36 Å / Num. all: 20716 / Num. obs: 20716 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 29.45 Å2 / Rmerge(I) obs: 0.079 / Net I/av σ(I): 8.4 / Net I/σ(I): 15.9
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZV6

2zv6


Resolution: 2.15→57.36 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.464 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23435 1059 5.1 %RANDOM
Rwork0.17441 ---
obs0.17741 19608 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.403 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å2-0 Å2-0 Å2
2---0.48 Å20 Å2
3----1.35 Å2
Refinement stepCycle: 1 / Resolution: 2.15→57.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2979 0 2 111 3092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193039
X-RAY DIFFRACTIONr_bond_other_d0.0010.022905
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.9524091
X-RAY DIFFRACTIONr_angle_other_deg0.83136701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5115364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58725.333150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.915568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2061510
X-RAY DIFFRACTIONr_chiral_restr0.1020.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023426
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02712
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5013.0151465
X-RAY DIFFRACTIONr_mcbond_other2.4993.0141464
X-RAY DIFFRACTIONr_mcangle_it3.5664.5021826
X-RAY DIFFRACTIONr_mcangle_other3.5674.5021827
X-RAY DIFFRACTIONr_scbond_it3.6733.5061574
X-RAY DIFFRACTIONr_scbond_other3.6693.5051574
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6075.0642265
X-RAY DIFFRACTIONr_long_range_B_refined7.15124.6613443
X-RAY DIFFRACTIONr_long_range_B_other7.13924.6053429
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 74 -
Rwork0.222 1430 -
obs--100 %

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