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- PDB-1e8a: The three-dimensional structure of human S100A12 -

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Basic information

Entry
Database: PDB / ID: 1e8a
TitleThe three-dimensional structure of human S100A12
ComponentsS100A12
KeywordsANTIFUNGAL PROTEIN / S100 PROTEIN / EF-HAND / CALCIUM BINDING
Function / homology
Function and homology information


mast cell activation / RAGE receptor binding / monocyte chemotaxis / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / endothelial cell migration / defense response to fungus / xenobiotic metabolic process / neutrophil chemotaxis / TAK1-dependent IKK and NF-kappa-B activation ...mast cell activation / RAGE receptor binding / monocyte chemotaxis / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / endothelial cell migration / defense response to fungus / xenobiotic metabolic process / neutrophil chemotaxis / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of MAP kinase activity / positive regulation of inflammatory response / calcium-dependent protein binding / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / secretory granule lumen / killing of cells of another organism / cytoskeleton / defense response to bacterium / inflammatory response / copper ion binding / innate immune response / calcium ion binding / Neutrophil degranulation / zinc ion binding / extracellular region / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 domain profile. / EF-hand domain / EF-hand domain pair ...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 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: 1.95 Å
AuthorsMoroz, O.V. / Antson, A.A. / Murshudov, G.N. / Maitland, N.J. / Dodson, G.G. / Wilson, K.S. / Skibshoj, I. / Lukanidin, E.M. / Bronstein, I.B.
Citation
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Human Calcium-Binding Protein S100A12
Authors: Moroz, O.V. / Antson, A.A. / Dodson, G.G. / Wilson, K.S. / Skibshoj, I. / Lukanidin, E. / Bronstein, I.
History
DepositionSep 18, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: S100A12
B: S100A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0826
Polymers20,9222
Non-polymers1604
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-76 kcal/mol
Surface area9700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.600, 99.600, 64.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein S100A12 / / CALGRANULIN C


Mass: 10460.834 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: GRANULOCYTE / Tissue: BLOOD / References: UniProt: P80511
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.9 Å3/Da / Density % sol: 57.9 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 20-25% PEG 5K MONOMETHYL ETHER, 0.2M CALCIUM CHLORIDE, 0.1M SODIUM CACODILATE, HANGING DROPS, pH 6.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15.0-8.0 mg/mlprotein1drop
20.1 Msodium cacodylate1reservoirpH6.5
30.2 M1reservoirCaCl2
420-25 %PEG5000 MME1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 17174 / % possible obs: 99.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.6
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.68 / % possible all: 99.1
Reflection shell
*PLUS
% possible obs: 99.1 % / Num. unique obs: 1721 / Rmerge(I) obs: 0.258

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MHO

1mho


Resolution: 1.95→25 Å / SU B: 4.36111 / SU ML: 0.12704 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28567 / ESU R Free: 0.19523
RfactorNum. reflection% reflectionSelection details
Rfree0.22 -5 %RANDOM
Rwork0.18 ---
obs-16326 100 %-
Displacement parametersBiso mean: 18.851 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å2-0.54 Å20 Å2
2---1.08 Å20 Å2
3---1.62 Å2
Refinement stepCycle: LAST / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1413 0 4 180 1597
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.021
X-RAY DIFFRACTIONp_angle_d1.741.93
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.421.5
X-RAY DIFFRACTIONp_mcangle_it0.792
X-RAY DIFFRACTIONp_scbond_it1.483
X-RAY DIFFRACTIONp_scangle_it2.494.5
X-RAY DIFFRACTIONp_plane_restr0.0070.02
X-RAY DIFFRACTIONp_chiral_restr0.150.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.851 Å2

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