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- PDB-1wy9: Crystal structure of microglia-specific protein, Iba1 -

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Basic information

Entry
Database: PDB / ID: 1wy9
TitleCrystal structure of microglia-specific protein, Iba1
ComponentsAllograft inflammatory factor 1
KeywordsMETAL BINDING PROTEIN / EF-hand / calucium binding
Function / homology
Function and homology information


positive regulation of muscle hyperplasia / positive regulation of chemokine production => GO:0032722 / cellular response to morphine / negative regulation of smooth muscle cell chemotaxis / positive regulation of smooth muscle cell chemotaxis / parallel actin filament bundle assembly / positive regulation of fibroblast growth factor production / cellular response to hydroperoxide / actin crosslink formation / : ...positive regulation of muscle hyperplasia / positive regulation of chemokine production => GO:0032722 / cellular response to morphine / negative regulation of smooth muscle cell chemotaxis / positive regulation of smooth muscle cell chemotaxis / parallel actin filament bundle assembly / positive regulation of fibroblast growth factor production / cellular response to hydroperoxide / actin crosslink formation / : / ruffle assembly / positive regulation of mononuclear cell migration / positive regulation of chemotaxis / positive regulation of monocyte chemotaxis / phagocytosis, engulfment / Rac protein signal transduction / phagocytic cup / actin filament bundle assembly / response to axon injury / positive regulation of T cell migration / positive regulation of G1/S transition of mitotic cell cycle / response to electrical stimulus / positive regulation of T cell proliferation / response to glucocorticoid / cellular response to hormone stimulus / ruffle / actin filament polymerization / cerebellum development / cell projection / actin filament / positive regulation of smooth muscle cell proliferation / negative regulation of smooth muscle cell proliferation / microglial cell activation / ruffle membrane / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of nitric oxide biosynthetic process / actin filament binding / lamellipodium / cellular response to oxidative stress / perikaryon / positive regulation of cell migration / inflammatory response / positive regulation of protein phosphorylation / negative regulation of gene expression / calcium ion binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Allograft inflammatory factor 1 / EF-hand / Recoverin; domain 1 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Allograft inflammatory factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsYamada, M. / Imai, Y. / Kohsaka, S. / Kamitori, S.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: X-ray Structures of the Microglia/Macrophage-specific Protein Iba1 from Human and Mouse Demonstrate Novel Molecular Conformation Change Induced by Calcium binding
Authors: Yamada, M. / Ohsawa, K. / Imai, Y. / Kohsaka, S. / Kamitori, S.
History
DepositionFeb 9, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: 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_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.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_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_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: Allograft inflammatory factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9792
Polymers16,9391
Non-polymers401
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Allograft inflammatory factor 1
hetero molecules

A: Allograft inflammatory factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9574
Polymers33,8772
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3690 Å2
ΔGint-60 kcal/mol
Surface area11720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)44.056, 44.056, 99.144
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Allograft inflammatory factor 1 / AIF-1 / Ionized calcium-binding adapter molecule 1 / Iba1


Mass: 16938.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aif1, Iba1 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: O70200
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.64 Å3/Da / Density % sol: 24.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M sodium citrate in 100mM HEPES-Na (pH 7.5), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A11
SYNCHROTRONPhoton Factory BL-6A21.03953, 1.03988, 1.04089
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 28, 2004
ADSC QUANTUM 42CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GraphiteSINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.039531
31.039881
41.040891
ReflectionResolution: 2.1→35.61 Å / Num. all: 6506 / Num. obs: 6506 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.9 Å2
Reflection shellResolution: 2.1→2.23 Å / % possible all: 75.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→35.61 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 322965.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS1.1
RfactorNum. reflection% reflectionSelection details
Rfree0.251 707 10.9 %RANDOM
Rwork0.217 ---
obs0.217 6506 93.7 %-
all-6506 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.7974 Å2 / ksol: 0.376511 e/Å3
Displacement parametersBiso mean: 39.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.52 Å23.3 Å20 Å2
2--5.06 Å20 Å2
3----11.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.1→35.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms911 0 1 53 965
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_improper_angle_d0.67
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 82 9.7 %
Rwork0.277 761 -
obs--75.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER_REP.PARAM
X-RAY DIFFRACTION4WATER_REP.PARAM

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