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- PDB-2d4h: Crystal-structure of the N-terminal large GTPase Domain of human ... -

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Basic information

Entry
Database: PDB / ID: 2d4h
TitleCrystal-structure of the N-terminal large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GMP
ComponentsInterferon-induced guanylate-binding protein 1
KeywordsSIGNALING PROTEIN / Protein- guanine nucleotide complex
Function / homology
Function and homology information


GDP phosphatase activity / non-canonical inflammasome complex assembly / protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane / negative regulation of T cell receptor signaling pathway / negative regulation of interleukin-2 production ...GDP phosphatase activity / non-canonical inflammasome complex assembly / protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane / negative regulation of T cell receptor signaling pathway / negative regulation of interleukin-2 production / spectrin binding / defense response to protozoan / cytokine binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / cellular response to interleukin-1 / regulation of protein localization to plasma membrane / negative regulation of protein localization to plasma membrane / regulation of calcium-mediated signaling / lipopolysaccharide binding / Hsp90 protein binding / cytoplasmic vesicle membrane / G protein activity / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / Interferon gamma signaling / GDP binding / actin cytoskeleton / cellular response to tumor necrosis factor / actin binding / cytoplasmic vesicle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / defense response to virus / defense response to bacterium / Golgi membrane / innate immune response / GTPase activity / GTP binding / Golgi apparatus / enzyme binding / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-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
GUANOSINE-5'-MONOPHOSPHATE / Guanylate-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGhosh, A. / Praefcke, G.J.K. / Renault, L. / Wittinghofer, A. / Herrmann, C.
Citation
Journal: Nature / Year: 2006
Title: How guanylate-binding proteins achieve assembly-stimulated processive cleavage of GTP to GMP.
Authors: Ghosh, A. / Praefcke, G.J. / Renault, L. / Wittinghofer, A. / Herrmann, C.
#1: Journal: Embo J. / Year: 2000
Title: Triphosphate structure of guanylate-binding protein 1 and implications for nucleotide binding and GTPase mechanism.
Authors: Prakash, B. / Renault, L. / Praefcke, G.J. / Herrmann, C. / Wittinghofer, A.
#2: Journal: Nature / Year: 2000
Title: Structure of human guanylate-binding protein 1 representing a unique class of GTP-binding proteins.
Authors: Prakash, B. / Praefcke, G.J. / Renault, L. / Herrmann, C. / Wittinghofer, A.
History
DepositionOct 19, 2005Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Aug 23, 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 / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Interferon-induced guanylate-binding protein 1
B: Interferon-induced guanylate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8834
Polymers74,1572
Non-polymers7262
Water2,144119
1
A: Interferon-induced guanylate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4422
Polymers37,0781
Non-polymers3631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interferon-induced guanylate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4422
Polymers37,0781
Non-polymers3631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.921, 173.450, 49.632
Angle α, β, γ (deg.)90.00, 110.85, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLU4AA7 - 31318 - 324
21METMETCYSCYS4BB7 - 31118 - 322
325GP5GP5GP5GP1AC593
425GP5GP5GP5GP1BD593
DetailsTwo biological assemblies are in the asymmetric unit

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Components

#1: Protein Interferon-induced guanylate-binding protein 1 / GTP-binding protein 1 / Guanine nucleotide-binding protein 1 / HuGBP-1


Mass: 37078.449 Da / Num. of mol.: 2 / Fragment: N-terminal Large GTPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBP1 / Plasmid: pQE9 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P32455
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 298 K
Details: 20% Peg 3350, 130 mM NH4NO3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 11, 2002
RadiationMonochromator: MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 14479 / % possible obs: 97.2 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.9→2.95 Å / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2B8W

2b8w


Resolution: 2.9→19.92 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.865 / SU B: 19.337 / SU ML: 0.37 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.492 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.275 718 5.2 %RANDOM
Rwork0.233 ---
obs0.235 13093 99.2 %-
all-13093 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.3 Å2
2---1.38 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4611 0 48 119 4778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224762
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9641.9816447
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1115575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0550.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023498
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.22414
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2202
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.292
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6281.52902
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16424699
X-RAY DIFFRACTIONr_scbond_it0.85431860
X-RAY DIFFRACTIONr_scangle_it1.5924.51748
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
33tight positional0.090.05
4302medium positional0.740.5
33tight thermal0.250.5
4302medium thermal3.072
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.357 61
Rwork0.301 939
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.18750.15580.21511.07430.00980.5463-0.0164-0.00120.01250.03720.00740.0028-0.0026-0.03140.0090.01350.0050.01660.08410.00710.03419.37150.514915.1662
20.2801-0.1982-0.03062.0009-0.23461.1923-0.0348-0.07720.0128-0.02260.0262-0.00220.1438-0.06080.00860.05410.0398-0.00360.0598-0.00110.0555.989744.75625.561
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 31618 - 327
2X-RAY DIFFRACTION2BB7 - 31118 - 322

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