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- PDB-2wcb: S100A12 complex with zinc in the absence of calcium -

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Basic information

Entry
Database: PDB / ID: 2wcb
TitleS100A12 complex with zinc in the absence of calcium
ComponentsPROTEIN S100-A12
KeywordsMETAL BINDING PROTEIN / CALCIUM SIGNALLING / 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 / xenobiotic metabolic process / neutrophil chemotaxis / 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 / xenobiotic metabolic process / neutrophil chemotaxis / 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 / extracellular space / 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: 1.73 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 10, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7636
Polymers21,5862
Non-polymers1774
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-126.35 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.696, 83.743, 155.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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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.: 2 / 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.21 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 7.5
Details: 34% PEG 3350, MME, 0.2M TRI AMMONIUM CITRATE PH 7.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.25
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
ReflectionResolution: 1.73→77.8 Å / Num. obs: 28275 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.1
Reflection shellHighest resolution: 1.73 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0082refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E8A

1e8a


Resolution: 1.73→77.85 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.668 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1429 5.1 %RANDOM
Rwork0.226 ---
obs0.228 26795 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.11 Å2
Baniso -1Baniso -2Baniso -3
1-6.04 Å20 Å20 Å2
2---2.5 Å20 Å2
3----3.54 Å2
Refinement stepCycle: LAST / Resolution: 1.73→77.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 4 166 1632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211545
X-RAY DIFFRACTIONr_bond_other_d0.0020.02994
X-RAY DIFFRACTIONr_angle_refined_deg1.831.9272095
X-RAY DIFFRACTIONr_angle_other_deg1.11432453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6165194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3812680
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87815276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.884152
X-RAY DIFFRACTIONr_chiral_restr0.1210.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021755
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02300
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_it0.9651.5946
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46221526
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4253599
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.584.5569
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: 1.73→1.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 107 -
Rwork0.354 1830 -
obs--95.75 %
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)
11.455-0.63-0.88176.75045.49676.52870.16250.17290.1348-0.68760.0403-0.1468-0.09630.0966-0.20280.19950.0319-0.00040.1646-0.01010.128117.82868.23519.4375
21.2041-0.01360.26313.88082.68563.2050.1139-0.0615-0.27420.49310.1198-0.33470.9670.3335-0.23370.36480.0921-0.05410.22550.00550.27622.8394-3.259317.8777
33.4089-3.0515-2.153810.22278.25078.68630.28590.2839-0.08070.0739-0.023-0.4023-0.42340.3211-0.26290.1778-0.0391-0.0490.09730.00240.060821.44313.837120.415
41.73070.41972.30132.11882.49217.44180.0282-0.1131-0.09470.2958-0.20420.47090.0928-0.79410.1760.0665-0.00560.06350.2528-0.0060.26826.933312.540322.3303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 19
2X-RAY DIFFRACTION2A20 - 91
3X-RAY DIFFRACTION3B0 - 19
4X-RAY DIFFRACTION4B20 - 90

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