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- PDB-8sjc: Crystal structure of Zn2+ bound calprotectin -

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Basic information

Entry
Database: PDB / ID: 8sjc
TitleCrystal structure of Zn2+ bound calprotectin
Components(Protein S100- ...) x 2
KeywordsANTIMICROBIAL PROTEIN / METAL BINDING PROTEIN
Function / homology
Function and homology information


S100A9 complex / regulation of integrin biosynthetic process / sequestering of zinc ion / calprotectin complex / neutrophil aggregation / positive regulation of peptide secretion / regulation of respiratory burst involved in inflammatory response / modulation of process of another organism / autocrine signaling / Toll-like receptor 4 binding ...S100A9 complex / regulation of integrin biosynthetic process / sequestering of zinc ion / calprotectin complex / neutrophil aggregation / positive regulation of peptide secretion / regulation of respiratory burst involved in inflammatory response / modulation of process of another organism / autocrine signaling / Toll-like receptor 4 binding / chronic inflammatory response / peptidyl-cysteine S-trans-nitrosylation / Metal sequestration by antimicrobial proteins / peptide secretion / leukocyte migration involved in inflammatory response / RAGE receptor binding / Regulation of TLR by endogenous ligand / astrocyte development / MyD88 deficiency (TLR2/4) / arachidonic acid binding / intermediate filament cytoskeleton / 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 / peptidyl-cysteine S-nitrosylation / antioxidant activity / RHO GTPases Activate NADPH Oxidases / endothelial cell migration / defense response to fungus / positive regulation of intrinsic apoptotic signaling pathway / neutrophil chemotaxis / autophagy / positive regulation of neuron projection development / positive regulation of inflammatory response / antimicrobial humoral immune response mediated by antimicrobial peptide / calcium-dependent protein binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / positive regulation of cell growth / microtubule binding / secretory granule lumen / response to ethanol / collagen-containing extracellular matrix / response to lipopolysaccharide / cytoskeleton / defense response to bacterium / inflammatory response / innate immune response / apoptotic process / calcium ion binding / Neutrophil degranulation / extracellular space / zinc ion binding / extracellular exosome / extracellular region / 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, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Protein S100-A8 / Protein S100-A9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsPerera, Y.R. / Garcia, V. / Guillen, R.M. / Chazin, W.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 AI127793 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)AI101171 United States
CitationJournal: To Be Published
Title: Crystal structure of Zn2+ bound calprotectin
Authors: Perera, Y.R. / Garcia, V. / Guillen, R.M. / Chazin, W.J.
History
DepositionApr 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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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-A9
D: Protein S100-A9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,17218
Polymers45,3944
Non-polymers77814
Water5,332296
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.611, 114.611, 53.182
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

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Protein S100- ... , 2 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 / MRP-8 / p8 / S100 calcium-binding protein A8 / Urinary stone protein band A


Mass: 10095.717 Da / Num. of mol.: 2 / Mutation: C42S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A8, CAGA, CFAG, MRP8 / Production host: Escherichia coli (E. coli) / References: UniProt: P05109
#2: Protein Protein S100-A9 / Calgranulin-B / Calprotectin L1H subunit / Leukocyte L1 complex heavy chain / Migration inhibitory ...Calgranulin-B / Calprotectin L1H subunit / Leukocyte L1 complex heavy chain / Migration inhibitory factor-related protein 14 / MRP-14 / p14 / S100 calcium-binding protein A9


Mass: 12601.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A9, CAGB, CFAG, MRP14 / Production host: Escherichia coli (E. coli) / References: UniProt: P06702

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Non-polymers , 5 types, 310 molecules

#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.0 M sodium citrate (pH 5.2), 28% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.87→57.31 Å / Num. obs: 65822 / % possible obs: 99.92 % / Redundancy: 6.6 % / Biso Wilson estimate: 25.21 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.67
Reflection shellResolution: 1.87→1.91 Å / Num. unique obs: 65822 / Rrim(I) all: 0.05334

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
PHENIX1.2phasing
Coot0.9.6model building
PHENIX1.2refinement
HKL-2000data reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→49.63 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1968 1671 5.02 %
Rwork0.1645 --
obs0.1662 33275 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 29 297 3469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052332
X-RAY DIFFRACTIONf_angle_d0.8384313
X-RAY DIFFRACTIONf_dihedral_angle_d6.43409
X-RAY DIFFRACTIONf_chiral_restr0.042463
X-RAY DIFFRACTIONf_plane_restr0.006551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.920.39091360.31282562X-RAY DIFFRACTION98
1.91-4.270.17461350.16512733X-RAY DIFFRACTION100
1.92-1.980.33121360.25092636X-RAY DIFFRACTION100
1.98-2.050.28071200.22212621X-RAY DIFFRACTION100
2.05-2.140.24011370.19132639X-RAY DIFFRACTION100
2.14-2.230.2121500.17742621X-RAY DIFFRACTION100
2.23-2.350.1791470.15442587X-RAY DIFFRACTION100
2.35-2.50.17851390.152629X-RAY DIFFRACTION100
2.5-2.690.21691470.14682637X-RAY DIFFRACTION100
2.69-2.960.19151300.17092648X-RAY DIFFRACTION100
2.96-3.390.1841580.15292630X-RAY DIFFRACTION100
3.39-4.270.16131360.13012661X-RAY DIFFRACTION100
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)
10.5092-1.31511.21727.6556-6.59296.4689-0.0528-0.1111-0.0290.26370.26760.3008-0.2092-0.3312-0.27450.1640.03060.00320.1928-0.01690.1824-43.029-21.0615.452
22.9212-2.21842.53496.3313-3.51118.0776-0.2228-0.07320.40520.5773-0.0011-0.3621-1.0141-0.00820.13770.27310.0159-0.02160.1388-0.03260.2246-35.393-9.3533.367
33.57281.3661-1.98464.8556-2.85652.12730.042-0.74760.36130.76930.0439-0.4706-0.61740.5297-0.09770.3836-0.0521-0.10620.3913-0.03940.3702-25.819-11.289.758
44.83481.03612.76215.08853.32233.19280.0073-0.0256-0.07210.11750.2329-0.4496-0.29920.338-0.21750.221-0.00440.00740.19360.00970.2011-29.612-15.546-4.833
58.1291-0.55353.65635.6289-0.07642.1570.0806-0.3335-0.03160.32960.0878-0.3608-0.0376-0.2381-0.11720.17930.0299-0.01590.14750.00580.1755-28.431-22.5258.09
64.0462-1.4793.07390.5501-1.33034.4260.20930.2712-0.1303-0.1312-0.07160.02960.26440.1713-0.20810.19130.0289-0.00230.1464-0.00830.1797-25.8-40.255-11.063
76.0464-2.84621.62244.1989-2.56322.0892-0.13850.11880.21320.0204-0.0924-0.4710.33770.8980.19830.2220.0249-0.00910.280.00420.2191-13.247-33.987-9.022
82.43680.5218-1.0143.7182-1.5229.5301-0.02420.04740.1948-0.1679-0.0473-0.202-0.28330.63890.03720.16930.0052-0.00070.20730.01370.221-17.125-26.389-6.04
95.1748-1.54291.38818.7294-4.95183.17150.08320.20.2924-0.12860.1110.1867-0.29370.0811-0.12560.18840.0020.00510.166-0.00370.2035-25.559-26.096-12.847
103.6438-3.36342.47144.1464-4.11954.4433-0.1872-0.0330.2250.46430.004-0.2872-0.4108-0.00380.21170.26720.0294-0.00620.194-0.01020.1733-33.15-25.26918.188
118.2913-1.92061.42832.6630.84444.8368-0.0293-0.6092-0.2180.14730.14260.00110.37730.3079-0.09390.27620.05040.03880.25650.03760.1864-29.136-40.03219.65
125.522-1.9911-0.89399.91762.85225.5227-0.14320.1958-0.5930.0418-0.01540.55430.2069-0.28160.15110.19850.01470.0150.22530.01290.3094-42.266-42.42811.022
132.81632.76851.78025.39660.74813.83460.03160.0375-0.41840.0270.05660.14860.32410.0739-0.07490.22360.04950.00850.18880.01150.2393-26.817-43.369.059
143.5033-2.36114.532.2088-2.14886.27930.0419-0.0072-0.29530.01990.08040.22930.1531-0.1408-0.1660.1787-0.00540.01540.13250.00440.1805-41.134-29.6212.382
156.7249-6.75676.16386.7913-6.20445.6824-0.1698-0.9751-1.07650.25641.02160.82040.1922-1.1808-0.83870.29410.01940.0360.41080.09880.3816-50.137-33.1666.018
168.9404-4.72473.79024.1586-1.78424.4389-0.04580.30070.1244-0.0293-0.0217-0.1939-0.17850.29420.04520.19520.00870.01640.2044-0.00060.153-28.966-29.988-23.777
173.7089-2.4689-2.44119.791-2.72213.9170.73310.56010.1644-0.983-0.6847-0.5553-0.75580.0333-0.06080.44870.12610.02660.2764-0.00980.2511-40.517-18.775-27.192
185.7601-1.79440.70111.7995-0.36517.30210.21390.4656-0.1031-0.8976-0.30720.722-0.5584-0.2590.13840.22360.0567-0.06990.2148-0.01570.25-45.667-29.324-23.476
192.47631.4998-1.01382.50331.24652.5955-0.06730.1107-0.66640.24640.09140.37420.3813-0.84580.1690.23780.00870.00210.34010.01680.3447-44.594-37.68-17.186
203.48145.2373-0.81068.1813-1.73018.6068-0.26640.162-0.00050.02990.11830.31870.2247-0.8220.22220.2030.00460.02260.2637-0.06340.2437-49.154-25.574-13.447
212.1061-3.6533-0.63926.97622.72597.44630.08510.41880.1012-0.261-0.29390.291-0.3111-0.43480.17110.24480.016-0.01420.2189-0.01290.2059-42.528-16.53-16.107
220.5733-1.44891.25674.4169-4.66565.01040.00730.0017-0.0590.24180.08240.1761-0.1882-0.0994-0.0620.16480.02920.00660.2023-0.01830.1956-35.135-32.511-10.809
235.22752.599-4.42824.0941-0.57734.649-0.2465-0.5488-0.88270.3426-0.1030.29410.51130.4680.36040.3040.04920.05410.22980.04120.3535-31.551-49.066-1.025
245.3477-4.48785.11533.7595-4.25614.94080.35580.1219-1.233-0.61380.3621.53111.1843-0.5496-0.73630.3481-0.0579-0.1130.28550.00890.4182-38.233-46.488-11.803
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:30 )A1 - 30
2X-RAY DIFFRACTION2( CHAIN A AND RESID 31:41 )A31 - 41
3X-RAY DIFFRACTION3( CHAIN A AND RESID 42:50 )A42 - 50
4X-RAY DIFFRACTION4( CHAIN A AND RESID 51:67 )A51 - 67
5X-RAY DIFFRACTION5( CHAIN A AND RESID 68:87 )A68 - 87
6X-RAY DIFFRACTION6( CHAIN B AND RESID 1:30 )B1 - 30
7X-RAY DIFFRACTION7( CHAIN B AND RESID 31:41 )B31 - 41
8X-RAY DIFFRACTION8( CHAIN B AND RESID 42:67 )B42 - 67
9X-RAY DIFFRACTION9( CHAIN B AND RESID 68:86 )B68 - 86
10X-RAY DIFFRACTION10( CHAIN C AND RESID 5:23 )C5 - 23
11X-RAY DIFFRACTION11( CHAIN C AND RESID 24:44 )C24 - 44
12X-RAY DIFFRACTION12( CHAIN C AND RESID 45:55 )C45 - 55
13X-RAY DIFFRACTION13( CHAIN C AND RESID 56:75 )C56 - 75
14X-RAY DIFFRACTION14( CHAIN C AND RESID 76:105 )C76 - 105
15X-RAY DIFFRACTION15( CHAIN C AND RESID 106:108 )C106 - 108
16X-RAY DIFFRACTION16( CHAIN D AND RESID 5:23 )D5 - 23
17X-RAY DIFFRACTION17( CHAIN D AND RESID 24:33 )D24 - 33
18X-RAY DIFFRACTION18( CHAIN D AND RESID 34:44 )D34 - 44
19X-RAY DIFFRACTION19( CHAIN D AND RESID 45:55 )D45 - 55
20X-RAY DIFFRACTION20( CHAIN D AND RESID 56:66 )D56 - 66
21X-RAY DIFFRACTION21( CHAIN D AND RESID 67:75 )D67 - 75
22X-RAY DIFFRACTION22( CHAIN D AND RESID 76:95 )D76 - 95
23X-RAY DIFFRACTION23( CHAIN D AND RESID 96:105 )D96 - 105
24X-RAY DIFFRACTION24( CHAIN D AND RESID 106:108 )D106 - 108

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