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- PDB-4idp: human atlastin-1 1-446, N440T, GppNHp -

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Basic information

Entry
Database: PDB / ID: 4idp
Titlehuman atlastin-1 1-446, N440T, GppNHp
ComponentsAtlastin-1
KeywordsHYDROLASE / GTPase / GTP/GDP binding
Function / homology
Function and homology information


endoplasmic reticulum tubular network membrane organization / endoplasmic reticulum tubular network membrane / Golgi cis cisterna / endoplasmic reticulum tubular network / endoplasmic reticulum organization / axonogenesis / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein homooligomerization / Golgi membrane / axon ...endoplasmic reticulum tubular network membrane organization / endoplasmic reticulum tubular network membrane / Golgi cis cisterna / endoplasmic reticulum tubular network / endoplasmic reticulum organization / axonogenesis / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein homooligomerization / Golgi membrane / axon / GTPase activity / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / endoplasmic reticulum / identical protein binding / membrane
Similarity search - Function
AHSP / 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. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold ...AHSP / 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. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Atlastin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.587 Å
AuthorsByrnes, L.J. / Singh, A. / Szeto, K. / Benvin, N.M. / O'Donnell, J.P. / Zipfel, W.R. / Sondermann, H.
CitationJournal: Embo J. / Year: 2013
Title: Structural basis for conformational switching and GTP loading of the large G protein atlastin.
Authors: Byrnes, L.J. / Singh, A. / Szeto, K. / Benvin, N.M. / O'Donnell, J.P. / Zipfel, W.R. / Sondermann, H.
History
DepositionDec 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Sep 20, 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 / struct_conn / 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 / _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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Atlastin-1
B: Atlastin-1
C: Atlastin-1
D: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,22612
Polymers207,0404
Non-polymers2,1868
Water7,260403
1
A: Atlastin-1
B: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6136
Polymers103,5202
Non-polymers1,0934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9850 Å2
ΔGint-64 kcal/mol
Surface area34260 Å2
MethodPISA
2
C: Atlastin-1
D: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6136
Polymers103,5202
Non-polymers1,0934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-63 kcal/mol
Surface area34150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.946, 268.121, 62.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Atlastin-1 / Brain-specific GTP-binding protein / GTP-binding protein 3 / GBP-3 / hGBP3 / Guanine nucleotide- ...Brain-specific GTP-binding protein / GTP-binding protein 3 / GBP-3 / hGBP3 / Guanine nucleotide-binding protein 3 / Spastic paraplegia 3 protein A


Mass: 51760.031 Da / Num. of mol.: 4 / Fragment: cytoplasmic domain (UNP residues 1-446) / Mutation: N440T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATL1, GBP3, SPG3A / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q8WXF7, 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.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.2 M lithium citrate tribasic tetrahydrate, 20% PEG3350, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 4, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.587→50 Å / Num. all: 69849 / Num. obs: 69639 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.8 % / Rsym value: 0.16 / Net I/σ(I): 12.3
Reflection shellResolution: 2.587→2.69 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.611 / % possible all: 97.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4IDQ

4idq


Resolution: 2.587→49.678 Å / SU ML: 0.29 / σ(F): 0.32 / Phase error: 32.25 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1985 3.52 %RANDOM
Rwork0.2012 ---
obs0.2025 56408 80.31 %-
all-69849 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.587→49.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13409 0 132 403 13944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01413911
X-RAY DIFFRACTIONf_angle_d1.67618813
X-RAY DIFFRACTIONf_dihedral_angle_d15.5295241
X-RAY DIFFRACTIONf_chiral_restr0.0982040
X-RAY DIFFRACTIONf_plane_restr0.012411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.587-2.65210.35311170.28163209X-RAY DIFFRACTION68
2.6521-2.72380.33011340.26793698X-RAY DIFFRACTION77
2.7238-2.80390.29711350.26413741X-RAY DIFFRACTION78
2.8039-2.89440.27531350.25683693X-RAY DIFFRACTION78
2.8944-2.99780.35011360.25773721X-RAY DIFFRACTION78
2.9978-3.11780.30241400.24423833X-RAY DIFFRACTION79
3.1178-3.25970.25581440.22653925X-RAY DIFFRACTION83
3.2597-3.43150.28061510.21554130X-RAY DIFFRACTION86
3.4315-3.64650.22481480.19824064X-RAY DIFFRACTION84
3.6465-3.92790.2221450.17973998X-RAY DIFFRACTION83
3.9279-4.3230.20991470.15973985X-RAY DIFFRACTION82
4.323-4.9480.13571460.154024X-RAY DIFFRACTION82
4.948-6.23210.20921510.1694131X-RAY DIFFRACTION83
6.2321-49.68740.18661560.17374271X-RAY DIFFRACTION83
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)
10.51680.1048-0.06940.39750.00480.3422-0.01080.0232-0.02270.0345-0.0035-0.0311-0.03720.027500.05240.0102-0.02970.07250.00630.0911-15.945951.3146-42.9128
20.2222-0.0414-0.02650.08760.10970.142-0.0509-0.04260.0103-0.5376-0.0210.3224-0.0011-0.0675-00.06940.0186-0.01810.0861-0.01060.1423-41.30616.141-51.2431
30.41740.0491-0.05110.28560.31830.40380.0117-0.02770.0572-0.0419-0.04270.1458-0.054-0.00900.0470.0293-0.03090.0810.00280.1164-49.8551.2288-49.2501
40.0264-0.0158-0.01810.0706-0.12970.0819-0.1193-0.0061-0.22910.0031-0.1436-0.51940.07820.079200.00990.1318-0.42720.01440.3158-0.9832-24.72196.2521-40.7792
50.4146-0.0840.09940.42530.01710.3657-0.01440.00080.0689-0.00050.0277-0.07950.03270.043100.05320.02260.0120.0695-0.02450.081-16.0573-26.5603-17.8842
60.21010.03840.25370.08840.17120.1071-0.00130.0027-0.04870.2437-0.02950.35610.0109-0.053700.2075-0.00750.02430.1145-0.02330.1063-41.219718.7292-9.6858
70.54330.2182-0.05120.5355-0.02370.3097-0.00020.00700.02590.0230.0378-0.0072-0.0323-00.0430.01440.00050.0667-0.00170.0357-50.0704-26.5614-11.7523
80.1031-0.04050.14860.0957-0.09460.0275-0.16120.0974-0.3475-0.404-0.1122-0.2132-0.080.1018-00.2717-0.0010.06160.09590.1011-0.3223-24.69618.6933-20.0281
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 31:347)
2X-RAY DIFFRACTION2(chain A and resid 348:446)
3X-RAY DIFFRACTION3(chain B and resid 31:347)
4X-RAY DIFFRACTION4(chain B and resid 348:446)
5X-RAY DIFFRACTION5(chain C and resid 31:347)
6X-RAY DIFFRACTION6(chain C and resid 348:446)
7X-RAY DIFFRACTION7(chain D and resid 30:347)
8X-RAY DIFFRACTION8(chain D and resid 348:446)

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