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- PDB-6zfe: Crystal structure of murine S100A9 mutant C80A bound to calcium a... -

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Basic information

Entry
Database: PDB / ID: 6zfe
TitleCrystal structure of murine S100A9 mutant C80A bound to calcium and zinc
ComponentsProtein S100-A9
KeywordsMETAL BINDING PROTEIN / Calcium-binding protein / homodimer / antimicrobial protein
Function / homology
Function and homology information


Metal sequestration by antimicrobial proteins / regulation of integrin biosynthetic process / neutrophil aggregation / positive regulation of peptide secretion / modulation of process of another organism / Regulation of TLR by endogenous ligand / : / autocrine signaling / chronic inflammatory response / peptidyl-cysteine S-trans-nitrosylation ...Metal sequestration by antimicrobial proteins / regulation of integrin biosynthetic process / neutrophil aggregation / positive regulation of peptide secretion / modulation of process of another organism / Regulation of TLR by endogenous ligand / : / autocrine signaling / chronic inflammatory response / peptidyl-cysteine S-trans-nitrosylation / RHO GTPases Activate NADPH Oxidases / leukocyte migration involved in inflammatory response / peptide secretion / astrocyte development / cornified envelope / leukocyte chemotaxis / peptidyl-cysteine S-nitrosylation / antioxidant activity / positive regulation of blood coagulation / positive regulation of intrinsic apoptotic signaling pathway / Neutrophil degranulation / neutrophil chemotaxis / autophagy / positive regulation of neuron projection development / positive regulation of inflammatory response / antimicrobial humoral immune response mediated by antimicrobial peptide / activation of cysteine-type endopeptidase activity involved in apoptotic process / calcium-dependent protein binding / cell junction / regulation of translation / response to lipopolysaccharide / cytoskeleton / innate immune response / apoptotic process / calcium ion binding / extracellular space / nucleoplasm / nucleus / 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 calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsParis, T. / Yatime, L.
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Divalent cations influence the dimerization mode of murine S100A9 protein by modulating its disulfide bond pattern.
Authors: Signor, L. / Paris, T. / Mas, C. / Picard, A. / Lutfalla, G. / Boeri Erba, E. / Yatime, L.
History
DepositionJun 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein S100-A9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6909
Polymers13,1681
Non-polymers5228
Water1086
1
A: Protein S100-A9
hetero molecules

A: Protein S100-A9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,38018
Polymers26,3362
Non-polymers1,04416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5480 Å2
ΔGint-309 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.610, 38.800, 53.170
Angle α, β, γ (deg.)90.000, 124.750, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-206-

SO4

21A-207-

SO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein S100-A9 / Calgranulin-B / Leukocyte L1 complex heavy chain / Migration inhibitory factor-related protein 14 / ...Calgranulin-B / Leukocyte L1 complex heavy chain / Migration inhibitory factor-related protein 14 / p14 / S100 calcium-binding protein A9


Mass: 13167.991 Da / Num. of mol.: 1 / Mutation: C80A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: S100a9, Cagb, Mrp14 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31725

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Non-polymers , 5 types, 14 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Ammonium sulfate, 2 mM spermine tetraHCl, 50 mM Bis-Tris, 40% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.2809 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2809 Å / Relative weight: 1
ReflectionResolution: 2.35→43.688 Å / Num. obs: 5224 / % possible obs: 98.5 % / Redundancy: 6.533 % / CC1/2: 0.997 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.132 / Χ2: 0.832 / Net I/σ(I): 8.73 / Num. measured all: 34129 / Scaling rejects: 28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.446.4960.7752.3335735585500.9010.84398.6
2.44-2.556.4940.6512.7736825775670.9320.70798.3
2.55-2.676.6430.4923.534815355240.9660.53597.9
2.67-2.826.5770.3534.634795345290.9720.38499.1
2.82-36.8870.2875.6635405205140.9820.31198.8
3-3.26.730.2137.2829414464370.9870.23198
3.2-3.46.2640.1349.921113373370.9940.146100
3.4-3.76.4440.10512.7824943953870.9950.11498
3.7-46.3370.0814.9717682812790.9970.08799.3
4-56.7040.0817.2634665265170.9970.08798.3
5-66.3390.08316.4715722502480.9950.09199.2
6-85.9520.07918.411131901870.9970.08798.4
8-106.3330.06523.543771690.9950.07197.2
10-156.4340.06124.3134155530.9990.06796.4
15-205.6670.0624.058514150.9990.066100
20-43.6884.1820.04120.5146121110.04691.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZDY

6zdy


Resolution: 2.35→43.688 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 42.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3054 526 10.12 %
Rwork0.268 4672 -
obs0.2718 5198 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.66 Å2 / Biso mean: 66.8568 Å2 / Biso min: 40.97 Å2
Refinement stepCycle: final / Resolution: 2.35→43.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms867 0 20 6 893
Biso mean--75.46 59.33 -
Num. residues----108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002895
X-RAY DIFFRACTIONf_angle_d0.4611198
X-RAY DIFFRACTIONf_chiral_restr0.052123
X-RAY DIFFRACTIONf_plane_restr0.002157
X-RAY DIFFRACTIONf_dihedral_angle_d19.295346
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3502-2.58670.48861420.422113298
2.5867-2.96090.39721270.3442115998
2.9609-3.73020.28681160.2653117399
3.7302-43.680.2551410.2199120899

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