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- PDB-2wcf: calcium-free (apo) S100A12 -

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Basic information

Entry
Database: PDB / ID: 2wcf
Titlecalcium-free (apo) S100A12
ComponentsPROTEIN S100-A12
KeywordsMETAL BINDING PROTEIN / CALCIUM SIGNALLING / APO / EF-HAND / CALCIUM FREE / S100 PROTEIN / HOST-PARASITE RESPONSE
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 / neutrophil chemotaxis / xenobiotic metabolic process / positive regulation of MAP kinase activity ...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 / neutrophil chemotaxis / xenobiotic metabolic process / positive regulation of MAP kinase activity / TAK1-dependent IKK and NF-kappa-B activation / 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 / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / 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: 2.78 Å
AuthorsMoroz, O.V. / Blagova, E.V. / Wilkinson, A.J. / Wilson, K.S. / Bronstein, I.B.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: The Crystal Structures of Human S100A12 in Apo Form and in Complex with Zinc: New Insights Into S100A12 Oligomerisation.
Authors: Moroz, O.V. / Blagova, E.V. / Wilkinson, A.J. / Wilson, K.S. / Bronstein, I.B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: The Three-Dimensional Structure of Human S100A12.
Authors: Moroz, 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.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of the Human S100A12-Copper Complex: Implications for Host-Parasite Defence.
Authors: Moroz, O.V. / Antson, A.A. / Grist, S.J. / Maitland, N.J. / Dodson, G.G. / Wilson, K.S. / Lukanidin, E. / Bronstein, I.B.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The Structure of S100A12 in a Hexameric Form and its Proposed Role in Receptor Signalling.
Authors: Moroz, O.V. / Antson, A.A. / Dodson, E.J. / Burrell, H.J. / Grist, S.J. / Lloyd, R.M. / Maitland, N.J. / Dodson, G.G. / Wilson, K.S. / Lukanidin, E. / Bronstein, I.B.
History
DepositionMar 11, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...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 / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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: PROTEIN S100-A12
B: PROTEIN S100-A12
C: PROTEIN S100-A12
D: PROTEIN S100-A12
E: PROTEIN S100-A12
F: PROTEIN S100-A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8058
Polymers64,7596
Non-polymers462
Water36020
1
A: PROTEIN S100-A12
B: PROTEIN S100-A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6093
Polymers21,5862
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-33.74 kcal/mol
Surface area8990 Å2
MethodPISA
2
C: PROTEIN S100-A12
D: PROTEIN S100-A12


Theoretical massNumber of molelcules
Total (without water)21,5862
Polymers21,5862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-27.85 kcal/mol
Surface area9130 Å2
MethodPISA
3
E: PROTEIN S100-A12
F: PROTEIN S100-A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6093
Polymers21,5862
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-36.64 kcal/mol
Surface area8610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.185, 93.197, 144.532
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
PROTEIN S100-A12 / S100 CALCIUM-BINDING PROTEIN A12 / CALGRANULIN-C / CGRP / NEUTROPHIL S100 PROTEIN / CALCIUM-BINDING ...S100 CALCIUM-BINDING PROTEIN A12 / CALGRANULIN-C / CGRP / NEUTROPHIL S100 PROTEIN / CALCIUM-BINDING PROTEIN IN AMNIOTIC FLUID 1 / P6 / CAGC / CAAF1 / S100A12 / CALCITERMIN


Mass: 10793.212 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE60 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P80511
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsEXTRA FOUR RESIDUES AT N TERMINUS MGGS

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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: 2.4 Å3/Da / Density % sol: 48.6 % / Description: NONE
Crystal growpH: 6 / Details: 25% PEG1500, 0.1M MMT PH6.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 15762 / % possible obs: 94.3 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.3
Reflection shellHighest resolution: 2.78 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.7 / % possible all: 70.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0082refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WCE

2wce


Resolution: 2.78→78.34 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.91 / SU B: 36.286 / SU ML: 0.321 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.323 785 5 %RANDOM
Rwork0.244 ---
obs0.248 14975 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.34 Å2
Baniso -1Baniso -2Baniso -3
1-47.33 Å20 Å20 Å2
2---36.76 Å20 Å2
3----10.57 Å2
Refinement stepCycle: LAST / Resolution: 2.78→78.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4052 0 2 20 4074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214340
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9061.9365847
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2835530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.26725.945217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.42915794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.797156
X-RAY DIFFRACTIONr_chiral_restr0.1340.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023200
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6661.52656
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23224255
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.95731684
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1724.51592
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.78→2.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 49 -
Rwork0.306 1019 -
obs--92.47 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.20850.63450.04385.0404-0.25983.90860.1072-0.05510.3239-0.0641-0.0207-0.2411-0.27160.2048-0.08660.43370.00650.02160.0254-0.03850.11147.581-10.572-36.124
21.73210.18390.32635.5822-1.10193.49380.0584-0.0589-0.0148-0.16040.0930.40360.1573-0.3543-0.15150.3221-0.0203-0.01990.12080.02760.0616-3.516-25.156-35.254
31.9065-1.3143-2.43125.62351.16165.3928-0.1824-0.27480.01440.59920.0561-0.36710.58220.46510.12630.58220.1589-0.02470.20790.05690.18917.104-35.695-46.098
45.04070.0777-1.64034.19180.56395.2199-0.02170.55860.56540.05540.0878-0.4117-0.48480.2063-0.06620.55280.0303-0.0160.22040.1310.211921.638-28.487-62.407
55.5515-1.1187-0.01597.6620.67381.12880.07790.0576-0.08840.07630.05251.1493-0.0906-0.2719-0.13040.3194-0.00170.04850.1970.11810.2589.36-52.093-78.515
63.0931-1.78550.24159.5967-1.18122.60160.2652-0.2267-0.21880.23110.2141-0.32730.20260.0688-0.47930.2622-0.0123-0.01310.21410.00110.176423.203-64.219-76.4
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 90
2X-RAY DIFFRACTION2B2 - 90
3X-RAY DIFFRACTION3C2 - 88
4X-RAY DIFFRACTION4D2 - 90
5X-RAY DIFFRACTION5E2 - 89
6X-RAY DIFFRACTION6F2 - 89

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