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- PDB-1irj: Crystal Structure of the MRP14 complexed with CHAPS -

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Basic information

Entry
Database: PDB / ID: 1irj
TitleCrystal Structure of the MRP14 complexed with CHAPS
ComponentsMigration Inhibitory Factor-Related Protein 14
KeywordsMETAL BINDING PROTEIN / Calgranulin B / MRP14 / S100A9 / EF-hand
Function / homology
Function and homology information


S100A9 complex / regulation of integrin biosynthetic process / sequestering of zinc ion / calprotectin complex / neutrophil aggregation / regulation of respiratory burst involved in inflammatory response / modulation of process of another organism / autocrine signaling / Toll-like receptor 4 binding / chronic inflammatory response ...S100A9 complex / regulation of integrin biosynthetic process / sequestering of zinc ion / calprotectin complex / neutrophil aggregation / 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 / Regulation of TLR by endogenous ligand / RAGE receptor binding / astrocyte development / MyD88 deficiency (TLR2/4) / arachidonic acid binding / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / regulation of toll-like receptor signaling pathway / regulation of cytoskeleton organization / 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 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsItou, H. / Yao, M. / Watanabe, N. / Nishihira, J. / Tanaka, I.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The crystal structure of human MRP14 (S100A9), a Ca(2+)-dependent regulator protein in inflammatory process.
Authors: Itou, H. / Yao, M. / Fujita, I. / Watanabe, N. / Suzuki, M. / Nishihira, J. / Tanaka, I.
History
DepositionOct 9, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Migration Inhibitory Factor-Related Protein 14
B: Migration Inhibitory Factor-Related Protein 14
C: Migration Inhibitory Factor-Related Protein 14
D: Migration Inhibitory Factor-Related Protein 14
E: Migration Inhibitory Factor-Related Protein 14
F: Migration Inhibitory Factor-Related Protein 14
G: Migration Inhibitory Factor-Related Protein 14
H: Migration Inhibitory Factor-Related Protein 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,16328
Polymers105,0638
Non-polymers3,10120
Water2,522140
1
A: Migration Inhibitory Factor-Related Protein 14
B: Migration Inhibitory Factor-Related Protein 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0417
Polymers26,2662
Non-polymers7755
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-76 kcal/mol
Surface area10110 Å2
MethodPISA
2
C: Migration Inhibitory Factor-Related Protein 14
D: Migration Inhibitory Factor-Related Protein 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6568
Polymers26,2662
Non-polymers1,3906
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-77 kcal/mol
Surface area9550 Å2
MethodPISA
3
E: Migration Inhibitory Factor-Related Protein 14
F: Migration Inhibitory Factor-Related Protein 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4266
Polymers26,2662
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-54 kcal/mol
Surface area9810 Å2
MethodPISA
4
G: Migration Inhibitory Factor-Related Protein 14
H: Migration Inhibitory Factor-Related Protein 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0417
Polymers26,2662
Non-polymers7755
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-77 kcal/mol
Surface area9920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.59, 178.44, 61.23
Angle α, β, γ (deg.)90, 113.17, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Migration Inhibitory Factor-Related Protein 14


Mass: 13132.824 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06702
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS / CHAPS detergent


Mass: 614.877 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 6000, CHAPS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Itou, H., (2001) Acta Crystallogr, D57, 1174. / PH range low: 8.2 / PH range high: 7.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mM1dropCaCl2
21 mMdithiothreitol1drop
310 mg/mlprotein1drop
40.1 MTris-HCl1reservoirpH7.8-8.2
51-2 %(w/v)PEG60001reservoir
60.25-1.75 %(w/v)CHAPS1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 30, 2000 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH AND SE-MAD WAVELENGTHS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 65554 / Num. obs: 65554 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 55.4 Å2 / Rsym value: 0.066 / Net I/σ(I): 6.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 9583 / Rsym value: 0.339 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 251869 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 99.7 % / Num. unique obs: 9583 / Num. measured obs: 37031 / Rmerge(I) obs: 0.339

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Processing

Software
NameVersionClassification
SHELXSphasing
SHARPphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→10 Å / Isotropic thermal model: Isotrophic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 6497 10 %RAMDOM
Rwork0.245 ---
all-65101 --
obs-64979 99.8 %-
Solvent computationBsol: 1.393 Å2 / ksol: 0.943 e/Å3
Displacement parametersBiso mean: 47.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.804 Å20 Å2-2.535 Å2
2--6.575 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5587 0 144 140 5871
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.228
X-RAY DIFFRACTIONc_dihedral_angle_d18.99
X-RAY DIFFRACTIONc_mcbond_it2.097
X-RAY DIFFRACTIONc_mcangle_it2.971
X-RAY DIFFRACTIONc_scbond_it3.219
X-RAY DIFFRACTIONc_scangle_it4.603
LS refinement shellResolution: 2.1→2.17 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.319 688 10.5 %
Rwork0.2899 5806 -
obs-6494 89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CPS.PARAMCPS.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.2449 / Rfactor Rfree: 0.2736
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.99
LS refinement shell
*PLUS
Rfactor Rfree: 0.319 / % reflection Rfree: 10.5 %

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