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- PDB-1odb: THE CRYSTAL STRUCTURE OF HUMAN S100A12 - COPPER COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1odb
TitleTHE CRYSTAL STRUCTURE OF HUMAN S100A12 - COPPER COMPLEX
ComponentsCALGRANULIN C
KeywordsMETAL BINDING PROTEIN / METAL-BINDING PROTEIN / CALCIUM-BINDING PROTEIN / S100 PROTEIN / EF-HAND / CALCIUM BINDING / HOST-PARASITE RESPONSE
Function / homology
Function and homology information


mast cell activation / RAGE receptor binding / positive regulation of MAP kinase activity / monocyte chemotaxis / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / defense response to fungus / endothelial cell migration / neutrophil chemotaxis / xenobiotic metabolic process ...mast cell activation / RAGE receptor binding / positive regulation of MAP kinase activity / monocyte chemotaxis / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / defense response to fungus / endothelial cell migration / neutrophil chemotaxis / xenobiotic metabolic process / positive regulation of NF-kappaB transcription factor activity / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of inflammatory response / antimicrobial humoral immune response mediated by antimicrobial peptide / calcium-dependent protein binding / secretory granule lumen / killing of cells of another organism / cytoskeleton / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / inflammatory response / copper ion binding / innate immune response / calcium ion binding / Neutrophil degranulation / extracellular region / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
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
COPPER (II) ION / Protein S100-A12
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsMoroz, O.V. / Antson, A.A. / Grist, S.J. / Maitland, N.J. / Dodson, G.G. / Wilson, K.S. / Lukanidin, E.M. / Bronstein, I.B.
Citation
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.M. / Bronstein, I.B.
History
DepositionFeb 15, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 29, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 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_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.ptnr1_symmetry / _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_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_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_conn.ptnr2_symmetry / _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: CALGRANULIN C
B: CALGRANULIN C
C: CALGRANULIN C
D: CALGRANULIN C
E: CALGRANULIN C
F: CALGRANULIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,62124
Polymers64,7596
Non-polymers86218
Water6,666370
1
C: CALGRANULIN C
D: CALGRANULIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8748
Polymers21,5862
Non-polymers2876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-101.94 kcal/mol
Surface area9050 Å2
MethodPISA
2
E: CALGRANULIN C
F: CALGRANULIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8748
Polymers21,5862
Non-polymers2876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-101.05 kcal/mol
Surface area9020 Å2
MethodPISA
3
A: CALGRANULIN C
B: CALGRANULIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8748
Polymers21,5862
Non-polymers2876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-96.53 kcal/mol
Surface area9670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.569, 118.957, 90.185
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
CALGRANULIN C / S100A12 / CAGC / P6 / CGRP / NEUTROPHIL S100 PROTEIN / CALCIUM-BINDING PROTEIN IN AMNIOTIC FLUID 1 / CAAF1


Mass: 10793.212 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: CA2+ AND CU2+ BOUND FORM / Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Cell: GRANULOCYTE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P80511
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINVOLVED IN HOST_PARASITE RESPONSE AGAINST ONCHOCERCA VOLVULUS AND BRUGIA MALAYI. EXISTS AS A ...INVOLVED IN HOST_PARASITE RESPONSE AGAINST ONCHOCERCA VOLVULUS AND BRUGIA MALAYI. EXISTS AS A DIMERIC AND IS MAINLY FOUND IN NEUTROPHILS.MEMBER OF THE S-100 FAMILY CONTAINING 2 EF-HAND CALCIUM-BINDING DOMAINS.
Sequence detailsRECLONING RESULTED IN ADDITIONAL MGGS CODONS AT N-TERMINUS

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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 Å3/Da / Density % sol: 58.1 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 5-7% PEG 5K MME, 250MM NACL, 5MM CACL2,1MM CUCL2,0.1M NA-CACODYLATE PH 6.5; HANGING-DROP VAPOUR DIFFUSION + SEEDING

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.373
DetectorDate: May 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.373 Å / Relative weight: 1
ReflectionResolution: 2.19→25 Å / Num. obs: 39556 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 18.1
Reflection shellResolution: 2.19→2.27 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.2 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E8A

1e8a


Resolution: 2.19→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.359 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1983 5 %RANDOM
Rwork0.186 ---
obs0.188 37532 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.59 Å2
Baniso -1Baniso -2Baniso -3
1--2.38 Å20 Å20 Å2
2--3.25 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.19→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4192 0 18 370 4580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214268
X-RAY DIFFRACTIONr_bond_other_d0.0030.023775
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9275767
X-RAY DIFFRACTIONr_angle_other_deg0.99938747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6365539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024821
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02833
X-RAY DIFFRACTIONr_nbd_refined0.2290.21246
X-RAY DIFFRACTIONr_nbd_other0.2310.24310
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0930.22390
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1080.249
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1820.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5131.52675
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95924254
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7231593
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8284.51513
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: 2.19→2.25 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.306 136
Rwork0.249 2556
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)
15.3756-0.1605-1.31770.83550.30045.007-0.12330.11730.58030.02530.14520.1039-0.3969-0.1792-0.02180.1424-0.0162-0.04750.03390.07160.152451.470842.02925.0321
25.0017-0.9083-2.96011.33061.07536.2582-0.25610.3981-0.51770.14480.04880.1520.5241-0.04920.20720.1463-0.0727-0.03540.12660.00270.1262.163529.051313.7708
36.3742-1.88783.60971.9573-2.52833.38790.13720.9591-0.3424-0.1927-0.2078-0.14890.34780.7010.07060.1218-0.05920.04770.3207-0.06640.097295.153627.694416.6477
44.8519-2.08111.99732.9175-2.7723.6333-0.17850.16560.67870.24-0.034-0.1767-0.53130.13440.21260.1783-0.12160.00680.14170.03380.125783.406543.676714.6206
54.24041.45470.53884.548-0.40144.3036-0.0429-0.1125-0.19090.05780.00880.2584-0.0984-0.26140.03410.1243-0.0506-0.01440.03020.03110.087788.404923.415240.7055
65.38233.2198-0.65926.0445-1.21591.2803-0.0151-0.1068-1.7211-0.3364-0.1426-0.43880.48710.12430.15760.3147-0.04750.01890.1474-0.00610.626986.66763.828337.8409
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 90
2X-RAY DIFFRACTION2B0 - 90
3X-RAY DIFFRACTION3C0 - 90
4X-RAY DIFFRACTION4D0 - 90
5X-RAY DIFFRACTION5E0 - 90
6X-RAY DIFFRACTION6F0 - 89

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