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- PDB-5hlo: Crystal structure of calcium and zinc-bound human S100A8 in space... -

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Basic information

Entry
Database: PDB / ID: 5hlo
TitleCrystal structure of calcium and zinc-bound human S100A8 in space group C2221
ComponentsProtein S100-A8
KeywordsSIGNALING PROTEIN / S100 protein / calcium / zinc / oligomer
Function / homology
Function and homology information


sequestering of zinc ion / neutrophil aggregation / calprotectin complex / positive regulation of peptide secretion / autocrine signaling / chronic inflammatory response / Metal sequestration by antimicrobial proteins / Toll-like receptor 4 binding / RAGE receptor binding / peptide secretion ...sequestering of zinc ion / neutrophil aggregation / calprotectin complex / positive regulation of peptide secretion / autocrine signaling / chronic inflammatory response / Metal sequestration by antimicrobial proteins / Toll-like receptor 4 binding / RAGE receptor binding / peptide secretion / leukocyte migration involved in inflammatory response / Regulation of TLR by endogenous ligand / astrocyte development / MyD88 deficiency (TLR2/4) / arachidonate binding / intermediate filament cytoskeleton / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / response to zinc ion / regulation of toll-like receptor signaling pathway / peptidyl-cysteine S-nitrosylation / regulation of cytoskeleton organization / RHO GTPases Activate NADPH Oxidases / defense response to fungus / positive regulation of intrinsic apoptotic signaling pathway / neutrophil chemotaxis / : / autophagy / positive regulation of inflammatory response / calcium-dependent protein binding / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / positive regulation of cell growth / microtubule binding / collagen-containing extracellular matrix / secretory granule lumen / response to ethanol / response to lipopolysaccharide / cytoskeleton / defense response to bacterium / inflammatory response / innate immune response / calcium ion binding / Neutrophil degranulation / apoptotic process / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleus / plasma membrane / 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 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...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 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / CACODYLATE ION / Protein S100-A8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLin, H. / Andersen, G.R. / Yatime, L.
CitationJournal: Bmc Struct.Biol. / Year: 2016
Title: Crystal structure of human S100A8 in complex with zinc and calcium.
Authors: Lin, H. / Andersen, G.R. / Yatime, L.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein S100-A8
B: Protein S100-A8
C: Protein S100-A8
D: Protein S100-A8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,33634
Polymers43,6984
Non-polymers1,63830
Water3,477193
1
A: Protein S100-A8
C: Protein S100-A8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,60916
Polymers21,8492
Non-polymers76014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-241 kcal/mol
Surface area9880 Å2
MethodPISA
2
B: Protein S100-A8
D: Protein S100-A8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,72718
Polymers21,8492
Non-polymers87816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-242 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.980, 90.030, 196.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-256-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Protein S100-A8 / Calgranulin-A / Calprotectin L1L subunit / Cystic fibrosis antigen / CFAG / Leukocyte L1 complex ...Calgranulin-A / Calprotectin L1L subunit / Cystic fibrosis antigen / CFAG / Leukocyte L1 complex light chain / Migration inhibitory factor-related protein 8 / p8 / S100 calcium-binding protein A8 / Urinary stone protein band A


Mass: 10924.606 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A8, CAGA, CFAG, MRP8 / Plasmid: pETM13 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05109

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Non-polymers , 6 types, 223 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 5 mM ZnCl2, 0.1 M Na cacodylate pH 6.5, 8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 29069 / % possible obs: 98.5 % / Redundancy: 8 % / Rsym value: 0.095 / Net I/σ(I): 16.47
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 3.04 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIXdev_1702refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MR8

1mr8


Resolution: 2.1→49.2 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1359 4.78 %random selection
Rwork0.1785 ---
obs0.1794 28412 96.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3009 0 50 193 3252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023088
X-RAY DIFFRACTIONf_angle_d0.5214148
X-RAY DIFFRACTIONf_dihedral_angle_d11.1651145
X-RAY DIFFRACTIONf_chiral_restr0.021458
X-RAY DIFFRACTIONf_plane_restr0.002521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.29261430.23092538X-RAY DIFFRACTION93
2.1751-2.26210.2681110.24982630X-RAY DIFFRACTION94
2.2621-2.36510.24651050.20672660X-RAY DIFFRACTION95
2.3651-2.48980.22891380.19992642X-RAY DIFFRACTION95
2.4898-2.64580.21111250.19662712X-RAY DIFFRACTION96
2.6458-2.850.21561290.19042672X-RAY DIFFRACTION97
2.85-3.13680.25191320.18882771X-RAY DIFFRACTION97
3.1368-3.59060.22181300.18012746X-RAY DIFFRACTION98
3.5906-4.52330.15721920.14012770X-RAY DIFFRACTION99
4.5233-49.21350.16891540.16922912X-RAY DIFFRACTION98
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
12.90020.29860.99041.5665-0.51225.86050.0097-0.5243-0.04520.00320.02380.20470.0743-0.694-0.02870.16670.00440.02340.40040.00820.2897chain A16.376216.5629-45.9426
20.41410.3380.28611.84651.13614.2225-0.0650.03830.1163-0.36570.1561-0.1623-0.93040.4695-0.0260.4322-0.07760.0230.26770.06190.3381chain B11.212812.435-100.3648
31.7065-0.22781.6141.7484-0.00245.1246-0.2657-0.05780.3971-0.08840.08320.0481-0.81970.11940.15720.2938-0.0346-0.05570.2826-0.00930.3557chain C18.428327.9177-61.3533
42.0367-0.2170.7311.96081.6056.34460.0173-0.09170.0658-0.1905-0.12110.2886-0.1525-0.65330.06010.2410.0055-0.02980.25290.00690.2965chain D-0.50269.1333-85.8617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:89
2X-RAY DIFFRACTION2chain B and resid 1:93
3X-RAY DIFFRACTION3chain C and resid 1:93
4X-RAY DIFFRACTION4chain D and resid 1:93

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