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- PDB-5fph: The GTPase domains of the immunity-related Irga6 dimerize in a pa... -

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Basic information

Entry
Database: PDB / ID: 5fph
TitleThe GTPase domains of the immunity-related Irga6 dimerize in a parallel head-to-head fashion
ComponentsINTERFERON-INDUCIBLE GTPASE 1
KeywordsHYDROLASE / IRGA6 / GMPPNP / INNATE IMMUNITY / IRG PROTEINS / GTPASE / DYNAMIN SUPERFAMILY / OLIGOMERIZATION
Function / homology
Function and homology information


symbiont-containing vacuole membrane / Golgi cisterna membrane / defense response to protozoan / cellular response to interferon-beta / response to bacterium / cytokine-mediated signaling pathway / GDP binding / nuclear membrane / defense response to Gram-negative bacterium / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement ...symbiont-containing vacuole membrane / Golgi cisterna membrane / defense response to protozoan / cellular response to interferon-beta / response to bacterium / cytokine-mediated signaling pathway / GDP binding / nuclear membrane / defense response to Gram-negative bacterium / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / regulation of autophagy / innate immune response / GTPase activity / endoplasmic reticulum membrane / GTP binding / identical protein binding / cytoplasm
Similarity search - Function
Immunity-related GTPases-like / : / Interferon-inducible GTPase (IIGP) / IRG-type guanine nucleotide-binding (G) domain / IRG-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Interferon-inducible GTPase 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSchulte, K. / Pawlowski, N. / Faelber, K. / Froehlich, C. / Howard, J. / Daumke, O.
CitationJournal: Bmc Biol. / Year: 2016
Title: The Immunity-Related Gtpase Irga6 Dimerizes in a Parallel Head-to-Head Fashion.
Authors: Schulte, K. / Pawlowski, N. / Faelber, K. / Froehlich, C. / Howard, J. / Daumke, O.
History
DepositionNov 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 2.0Aug 11, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site.pdbx_PDB_ins_code / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_ins_code / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _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 / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_sheet.id / _struct_sheet_order.sense / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 2.1Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650 HELIX DETERMINATION METHOD: AUTHOR
Remark 700 SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERFERON-INDUCIBLE GTPASE 1
B: INTERFERON-INDUCIBLE GTPASE 1
C: INTERFERON-INDUCIBLE GTPASE 1
D: INTERFERON-INDUCIBLE GTPASE 1
E: INTERFERON-INDUCIBLE GTPASE 1
F: INTERFERON-INDUCIBLE GTPASE 1
G: INTERFERON-INDUCIBLE GTPASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,49828
Polymers342,8047
Non-polymers3,69321
Water1448
1
A: INTERFERON-INDUCIBLE GTPASE 1
hetero molecules

A: INTERFERON-INDUCIBLE GTPASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0868
Polymers97,9442
Non-polymers1,1426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
2
B: INTERFERON-INDUCIBLE GTPASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5434
Polymers48,9721
Non-polymers5713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: INTERFERON-INDUCIBLE GTPASE 1
C: INTERFERON-INDUCIBLE GTPASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2089
Polymers97,9442
Non-polymers1,2647
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: INTERFERON-INDUCIBLE GTPASE 1
D: INTERFERON-INDUCIBLE GTPASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6617
Polymers97,9442
Non-polymers7175
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: INTERFERON-INDUCIBLE GTPASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6655
Polymers48,9721
Non-polymers6934
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
D: INTERFERON-INDUCIBLE GTPASE 1
F: INTERFERON-INDUCIBLE GTPASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5396
Polymers97,9442
Non-polymers5954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
F: INTERFERON-INDUCIBLE GTPASE 1
G: INTERFERON-INDUCIBLE GTPASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0868
Polymers97,9442
Non-polymers1,1426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.510, 98.510, 1289.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
INTERFERON-INDUCIBLE GTPASE 1 / IMMUNITY-RELATED GTPASE 6


Mass: 48972.047 Da / Num. of mol.: 7 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: Q9QZ85, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growDetails: 33% PEG 4000 3 % ISOPROPANOL 50 MM HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.972
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2012 / Details: 3 SILICON MIRRORS
RadiationMonochromator: SILICON DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 3.2→214.9 Å / Num. obs: 115430 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 15.82 % / Biso Wilson estimate: 75.35 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 13.12
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 6.81 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.74 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXPHASER MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TQ2

1tq2


Resolution: 3.2→68.978 Å / SU ML: 0.63 / σ(F): 1.36 / Phase error: 31.79 / Stereochemistry target values: ML
Details: FOLLOWING RESIDUES ARE DISORDERED CHAIN A 1-14, 200-202, 357 CHAIN B 1-14, 356-357 CHAIN C 1-14, 195-199, 333-334, 355-357 CHAIN D 1-13, 197-200 CHAIN E 1-13, 197-199, 356 CHAIN F 1-12, 105- ...Details: FOLLOWING RESIDUES ARE DISORDERED CHAIN A 1-14, 200-202, 357 CHAIN B 1-14, 356-357 CHAIN C 1-14, 195-199, 333-334, 355-357 CHAIN D 1-13, 197-200 CHAIN E 1-13, 197-199, 356 CHAIN F 1-12, 105-106, 196-198, 298, 356-357 CHAIN G 413
RfactorNum. reflection% reflection
Rfree0.3171 3215 5 %
Rwork0.2966 --
obs0.2977 64283 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→68.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22394 0 221 8 22623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323058
X-RAY DIFFRACTIONf_angle_d0.72231182
X-RAY DIFFRACTIONf_dihedral_angle_d12.5298696
X-RAY DIFFRACTIONf_chiral_restr0.0273499
X-RAY DIFFRACTIONf_plane_restr0.0043948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.24780.46021340.41482545X-RAY DIFFRACTION100
3.2478-3.29850.38911390.37872645X-RAY DIFFRACTION100
3.2985-3.35260.46361320.39182514X-RAY DIFFRACTION100
3.3526-3.41040.4081370.37652611X-RAY DIFFRACTION100
3.4104-3.47240.39621350.37312553X-RAY DIFFRACTION100
3.4724-3.53920.45821370.37962601X-RAY DIFFRACTION100
3.5392-3.61140.34611360.34412582X-RAY DIFFRACTION100
3.6114-3.690.37031340.33312557X-RAY DIFFRACTION100
3.69-3.77580.36711400.32512663X-RAY DIFFRACTION100
3.7758-3.87020.34541350.32452564X-RAY DIFFRACTION100
3.8702-3.97490.3441380.31572611X-RAY DIFFRACTION100
3.9749-4.09180.33421390.29552642X-RAY DIFFRACTION100
4.0918-4.22390.34921360.30452580X-RAY DIFFRACTION100
4.2239-4.37480.2911380.28282625X-RAY DIFFRACTION100
4.3748-4.54990.3211390.2842652X-RAY DIFFRACTION100
4.5499-4.7570.29431400.27672657X-RAY DIFFRACTION100
4.757-5.00770.26771410.26622679X-RAY DIFFRACTION100
5.0077-5.32130.29441400.27012658X-RAY DIFFRACTION100
5.3213-5.7320.28041420.28772707X-RAY DIFFRACTION100
5.732-6.30850.32961440.29972726X-RAY DIFFRACTION100
6.3085-7.22050.33161450.28812764X-RAY DIFFRACTION100
7.2205-9.09380.22511490.24272830X-RAY DIFFRACTION100
9.0938-68.99350.24461650.23553102X-RAY DIFFRACTION99

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