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- PDB-4xjk: Crystal structure of Mn(II) Ca(II) Na(I) bound calprotectin -

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Basic information

Entry
Database: PDB / ID: 4xjk
TitleCrystal structure of Mn(II) Ca(II) Na(I) bound calprotectin
Components(Protein S100- ...) x 2
KeywordsMETAL BINDING PROTEIN / EF-hand calcium binding / Metal ion binding / Immune system process / Inflammatory response
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 / leukocyte migration involved in inflammatory response / peptide secretion / Regulation of TLR by endogenous ligand / RAGE receptor binding / astrocyte development / MyD88 deficiency (TLR2/4) / arachidonic acid 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 / 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 / activation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / secretory granule lumen / collagen-containing extracellular matrix / response to ethanol / response to lipopolysaccharide / cytoskeleton / defense response to bacterium / inflammatory response / innate immune response / apoptotic process / calcium ion binding / Neutrophil degranulation / 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 / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...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, 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Protein S100-A8 / Protein S100-A9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsDrennan, C.L. / Bowman, S.E.J.
Funding support United States, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069857 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM099257 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
Department of Energy (DOE, United States)DE-AC02-06-CH11357 United States
National Science Foundation (NSF, United States)1352132 United States
National Institutes of Health/Office of the Director1DP2OD007045-01 United States
Department of Energy (DOE, United States)DE-FG02-11ER16282 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Manganese Binding Properties of Human Calprotectin under Conditions of High and Low Calcium: X-ray Crystallographic and Advanced Electron Paramagnetic Resonance Spectroscopic Analysis.
Authors: Gagnon, D.M. / Brophy, M.B. / Bowman, S.E. / Stich, T.A. / Drennan, C.L. / Britt, R.D. / Nolan, E.M.
History
DepositionJan 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: 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 / refine_hist / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_high / _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-A9
C: Protein S100-A8
D: Protein S100-A9
E: Protein S100-A8
F: Protein S100-A9
G: Protein S100-A8
H: Protein S100-A9
I: Protein S100-A8
J: Protein S100-A9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,33235
Polymers120,42710
Non-polymers90525
Water12,683704
1
A: Protein S100-A8
B: Protein S100-A9
C: Protein S100-A8
D: Protein S100-A9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,53314
Polymers48,1714
Non-polymers36210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint-186 kcal/mol
Surface area17660 Å2
MethodPISA
2
E: Protein S100-A8
F: Protein S100-A9
G: Protein S100-A8
H: Protein S100-A9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,53314
Polymers48,1714
Non-polymers36210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10770 Å2
ΔGint-183 kcal/mol
Surface area17570 Å2
MethodPISA
3
I: Protein S100-A8
J: Protein S100-A9
hetero molecules

I: Protein S100-A8
J: Protein S100-A9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,53314
Polymers48,1714
Non-polymers36210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_856-x+3,y,-z+11
Buried area10910 Å2
ΔGint-186 kcal/mol
Surface area17550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.279, 49.239, 218.067
Angle α, β, γ (deg.)90.000, 94.070, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-211-

HOH

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Components

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Protein S100- ... , 2 types, 10 molecules ACEGIBDFHJ

#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: 10837.463 Da / Num. of mol.: 5 / 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) / Strain (production host): BL21(DE3) / 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 / p14 / S100 calcium-binding protein A9


Mass: 13247.955 Da / Num. of mol.: 5 / Mutation: C3S
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) / Strain (production host): BL21(DE3) / References: UniProt: P06702

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Non-polymers , 4 types, 729 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Mutation: C42S
Source method: isolated from a genetically manipulated source
Formula: Ca
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 704 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: PEG 4000, isopropanol, sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 22, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 114052 / % possible obs: 97.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 25.18 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.026 / Rrim(I) all: 0.06 / Χ2: 0.972 / Net I/av σ(I): 26.833 / Net I/σ(I): 6.8 / Num. measured all: 561814
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.76-1.8240.515102700.8470.2750.5870.88888.9
1.82-1.94.80.435113870.9250.2180.4890.90697.9
1.9-1.9850.331114990.9520.1620.370.93399.2
1.98-2.095.10.231114360.9730.1130.2580.93299.1
2.09-2.224.70.153114530.9860.0780.1720.97998.1
2.22-2.395.30.119115470.9920.0570.1330.99899.2
2.39-2.635.10.09115840.9940.0440.1010.9999.1
2.63-3.0150.063114150.9960.0310.0711.0698.2
3.01-3.795.20.043116640.9980.020.0481.02298.8
3.79-5050.03117970.9990.0150.0340.97698.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
HKL-2000data reduction
PHASER2.5.5phasing
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GGF

4ggf


Resolution: 1.76→49.239 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 1887 1.76 %Random selection
Rwork0.1853 105389 --
obs0.1859 107276 91.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.4 Å2 / Biso mean: 35.1104 Å2 / Biso min: 14.84 Å2
Refinement stepCycle: final / Resolution: 1.76→49.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8062 0 25 704 8791
Biso mean--25.69 40.42 -
Num. residues----984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078381
X-RAY DIFFRACTIONf_angle_d0.93911274
X-RAY DIFFRACTIONf_chiral_restr0.0381198
X-RAY DIFFRACTIONf_plane_restr0.0051451
X-RAY DIFFRACTIONf_dihedral_angle_d14.0943193
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7595-1.8070.31841110.27156253636472
1.807-1.86020.3361340.26166863699779
1.8602-1.92030.27751250.24037509763485
1.9203-1.98890.3111370.22577833797089
1.9889-2.06850.22551520.21398040819292
2.0685-2.16270.251460.19698247839394
2.1627-2.27670.23131440.19368346849095
2.2767-2.41930.24251590.19048595875497
2.4193-2.60610.25911580.19288632879098
2.6061-2.86830.21151470.19458569871697
2.8683-3.28330.26071600.20058763892399
3.2833-4.13630.17641540.16458724887898
4.1363-49.25830.18571600.15769015917599

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