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

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Basic information

Entry
Database: PDB / ID: 5hlv
TitleCrystal structure of calcium and zinc-bound human S100A8 in space group P212121
ComponentsProtein S100-A8
KeywordsSIGNALING PROTEIN / S100 proteins / calcium / zinc / oligomer
Function / homology
Function and homology information


S100A8 complex / neutrophil aggregation / calprotectin complex / positive regulation of peptide secretion / autocrine signaling / chronic inflammatory response / Toll-like receptor 4 binding / peptidyl-cysteine S-nitrosylation / Metal sequestration by antimicrobial proteins / RAGE receptor binding ...S100A8 complex / neutrophil aggregation / calprotectin complex / positive regulation of peptide secretion / autocrine signaling / chronic inflammatory response / Toll-like receptor 4 binding / peptidyl-cysteine S-nitrosylation / Metal sequestration by antimicrobial proteins / RAGE receptor binding / peptide secretion / leukocyte migration involved in inflammatory response / Regulation of TLR by endogenous ligand / astrocyte development / intermediate filament cytoskeleton / MyD88 deficiency (TLR2/4) / arachidonate binding / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / regulation of toll-like receptor signaling pathway / response to zinc ion / regulation of cytoskeleton organization / RHO GTPases Activate NADPH Oxidases / defense response to fungus / endothelial cell migration / 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 / : / secretory granule lumen / response to lipopolysaccharide / response to ethanol / cytoskeleton / defense response to bacterium / inflammatory response / innate immune response / apoptotic process / calcium ion binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / zinc ion 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 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 / Protein S100-A8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
E: Protein S100-A8
F: Protein S100-A8
G: Protein S100-A8
H: Protein S100-A8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,98740
Polymers87,3978
Non-polymers1,59032
Water6,449358
1
A: Protein S100-A8
D: Protein S100-A8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,25810
Polymers21,8492
Non-polymers4098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-149 kcal/mol
Surface area9360 Å2
MethodPISA
2
B: Protein S100-A8
H: Protein S100-A8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,23510
Polymers21,8492
Non-polymers3868
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-165 kcal/mol
Surface area9410 Å2
MethodPISA
3
C: Protein S100-A8
E: Protein S100-A8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,25810
Polymers21,8492
Non-polymers4098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-156 kcal/mol
Surface area9280 Å2
MethodPISA
4
F: Protein S100-A8
G: Protein S100-A8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,23510
Polymers21,8492
Non-polymers3868
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-165 kcal/mol
Surface area9270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.930, 85.090, 197.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#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.: 8
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 , 5 types, 390 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.2 M ammonium acetate, 0.1 M Na acetate pH 4.0, 15% PEG 3350, 0.4% 2,2,2-trifluoroethanol

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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: 2.2→50 Å / Num. obs: 42972 / % possible obs: 96.5 % / Redundancy: 6.1 % / Rsym value: 0.148 / Net I/σ(I): 12.54
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.08 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MR8

1mr8


Resolution: 2.2→40.26 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 2038 4.87 %random selection
Rwork0.1819 ---
obs0.1836 41886 94.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5791 0 50 358 6199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025921
X-RAY DIFFRACTIONf_angle_d0.4397955
X-RAY DIFFRACTIONf_dihedral_angle_d20.192193
X-RAY DIFFRACTIONf_chiral_restr0.051886
X-RAY DIFFRACTIONf_plane_restr0.002994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25120.29391260.24972671X-RAY DIFFRACTION95
2.2512-2.30750.27661330.23132663X-RAY DIFFRACTION95
2.3075-2.36990.26231300.21922625X-RAY DIFFRACTION95
2.3699-2.43960.27281380.21472637X-RAY DIFFRACTION95
2.4396-2.51830.25551370.21282667X-RAY DIFFRACTION96
2.5183-2.60830.25061470.20132669X-RAY DIFFRACTION96
2.6083-2.71270.27431580.19962654X-RAY DIFFRACTION96
2.7127-2.83610.24811420.19962685X-RAY DIFFRACTION95
2.8361-2.98560.24221300.19712687X-RAY DIFFRACTION96
2.9856-3.17260.22481450.19982650X-RAY DIFFRACTION94
3.1726-3.41750.23531270.19582694X-RAY DIFFRACTION95
3.4175-3.76110.20511310.1682634X-RAY DIFFRACTION94
3.7611-4.30480.1531240.14122671X-RAY DIFFRACTION92
4.3048-5.42160.15841330.14192617X-RAY DIFFRACTION91
5.4216-40.26650.17521370.15672624X-RAY DIFFRACTION86
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)
12.0378-0.3722-0.50471.5169-0.98745.8963-0.01680.07650.04260.0752-0.02920.1064-0.1456-0.190.03430.12990.0080.00370.1152-0.0390.1591.1694-26.4221-5.2809
23.0494-0.34950.81851.0175-0.94726.22640.03140.0162-0.01460.00340.01040.1455-0.2228-0.3083-0.03050.15860.00770.03280.1246-0.0230.18524.0658-67.1378-37.8053
31.33-0.30021.67422.4314-1.47715.94140.06980.1701-0.2591-0.2213-0.03330.08770.53260.0694-0.04080.2080.02930.02020.1715-0.06080.21323.1259-49.6505-11.5268
41.86230.25040.78241.95050.13745.8626-0.04130.40950.0761-0.12040.0038-0.30040.01620.65330.020.149-0.02980.00940.27140.03750.1911.7643-27.8222-21.6281
52.43030.07540.50112.46030.7376.21290.02040.1762-0.0026-0.1154-0.0293-0.4078-0.16610.66360.00490.17030.00560.01950.22630.03760.204614.5633-46.10554.3933
63.8489-0.0381-0.51172.7521-0.41055.21060.05080.10650.51010.21-0.0503-0.2484-0.65680.2189-0.01050.2117-0.0361-0.03730.15370.01530.246126.4777-61.1566-27.0131
73.9324-0.60481.54781.07480.38656.01480.16330.6166-0.1816-0.1684-0.1297-0.13670.35210.7214-0.03750.1890.0580.02660.3512-0.02520.216527.0668-71.7678-43.5274
82.5298-0.94570.72872.3094-0.18185.49270.08050.17020.42690.1378-0.0585-0.2388-0.96290.7384-0.00620.3265-0.101-0.01320.3240.00930.25539.1318-56.2494-53.5408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:89
2X-RAY DIFFRACTION2chain B and resid 1:89
3X-RAY DIFFRACTION3chain C and resid 2:89
4X-RAY DIFFRACTION4chain D and resid 1:89
5X-RAY DIFFRACTION5chain E and resid 1:88
6X-RAY DIFFRACTION6chain F and resid 1:88
7X-RAY DIFFRACTION7chain G and resid 1:90
8X-RAY DIFFRACTION8chain H and resid 1:89

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