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- PDB-8sjb: Crystal structure of Zn2+ bound calprotectin variant H87C -

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Basic information

Entry
Database: PDB / ID: 8sjb
TitleCrystal structure of Zn2+ bound calprotectin variant H87C
Components(Protein S100- ...) x 2
KeywordsANTIMICROBIAL PROTEIN / METAL BINDING PROTEIN
Function / homology
Function and homology information


regulation of integrin biosynthetic process / S100A9 complex / sequestering of zinc ion / neutrophil aggregation / calprotectin complex / positive regulation of peptide secretion / modulation of process of another organism / regulation of respiratory burst involved in inflammatory response / autocrine signaling / chronic inflammatory response ...regulation of integrin biosynthetic process / S100A9 complex / sequestering of zinc ion / neutrophil aggregation / calprotectin complex / positive regulation of peptide secretion / modulation of process of another organism / regulation of respiratory burst involved in inflammatory response / autocrine signaling / chronic inflammatory response / peptidyl-cysteine S-trans-nitrosylation / Toll-like receptor 4 binding / Metal sequestration by antimicrobial proteins / 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 / antioxidant activity / endothelial cell migration / RHO GTPases Activate NADPH Oxidases / defense response to fungus / positive regulation of intrinsic apoptotic signaling pathway / neutrophil chemotaxis / : / positive regulation of neuron projection development / autophagy / positive regulation of inflammatory response / calcium-dependent protein binding / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / 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 / 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, 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: 1.74 Å
AuthorsPerera, Y.R. / Rodriguez, A.M. / 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. / Nassif, A.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

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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)44,77315
Polymers43,5584
Non-polymers1,21511
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10690 Å2
ΔGint-212 kcal/mol
Surface area17140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.436, 76.935, 106.793
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 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: 10141.738 Da / Num. of mol.: 2 / Mutation: H17N, H27N, C42S, H87C
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: 11637.075 Da / Num. of mol.: 2 / Mutation: H88N, H92N
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 , 4 types, 261 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 8.0, 0.05 M ammonium acetate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2822 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2822 Å / Relative weight: 1
ReflectionResolution: 1.74→62.42 Å / Num. obs: 50045 / % possible obs: 99.26 % / Redundancy: 6.6 % / Biso Wilson estimate: 33.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.4
Reflection shellResolution: 1.87→1.91 Å / Num. unique obs: 2106 / CC1/2: 0.689

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
Coot0.9.6model building
PHENIX1.2phasing
HKL-2000data reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→62.42 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1971 2564 5.12 %
Rwork0.1844 --
obs0.1852 50044 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→62.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2993 0 65 250 3308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121
X-RAY DIFFRACTIONf_angle_d1.0651
X-RAY DIFFRACTIONf_dihedral_angle_d10.879424
X-RAY DIFFRACTIONf_chiral_restr0.058456
X-RAY DIFFRACTIONf_plane_restr0.008531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.770.35591060.38452597X-RAY DIFFRACTION98
1.77-1.810.32931510.30942574X-RAY DIFFRACTION100
1.81-1.850.28581500.26322579X-RAY DIFFRACTION99
1.85-1.890.26671290.26162623X-RAY DIFFRACTION100
1.89-1.940.25481380.21752606X-RAY DIFFRACTION100
1.94-1.990.21141340.19662598X-RAY DIFFRACTION100
1.99-2.050.20881530.20262605X-RAY DIFFRACTION100
2.05-2.120.19041320.20752633X-RAY DIFFRACTION100
2.12-2.190.2231320.22212638X-RAY DIFFRACTION100
2.19-2.280.21961370.18392612X-RAY DIFFRACTION100
2.28-2.380.20561550.17992610X-RAY DIFFRACTION100
2.38-2.510.18991330.17452646X-RAY DIFFRACTION100
2.51-2.670.20351330.18952678X-RAY DIFFRACTION100
2.67-2.870.25441440.21012630X-RAY DIFFRACTION100
2.87-3.160.21291420.18932657X-RAY DIFFRACTION100
3.16-3.620.20251520.17752681X-RAY DIFFRACTION100
3.62-4.560.14041550.1432708X-RAY DIFFRACTION100
4.56-62.420.19111880.17742805X-RAY DIFFRACTION100

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