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- PDB-3ftq: Crystal structure of Septin 2 in complex with GppNHp and Mg2+ -

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Basic information

Entry
Database: PDB / ID: 3ftq
TitleCrystal structure of Septin 2 in complex with GppNHp and Mg2+
ComponentsSeptin-2
KeywordsCELL CYCLE / GTP binding / Filament / Cell division / GTP-binding / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


regulation of L-glutamate import across plasma membrane / sperm annulus / kinetochore => GO:0000776 / exocyst / protein localization => GO:0008104 / septin complex / ciliary transition zone / photoreceptor connecting cilium / actomyosin contractile ring / cytoskeleton-dependent cytokinesis ...regulation of L-glutamate import across plasma membrane / sperm annulus / kinetochore => GO:0000776 / exocyst / protein localization => GO:0008104 / septin complex / ciliary transition zone / photoreceptor connecting cilium / actomyosin contractile ring / cytoskeleton-dependent cytokinesis / Anchoring of the basal body to the plasma membrane / septin ring / regulation of exocytosis / non-motile cilium / ciliary membrane / smoothened signaling pathway / intercellular bridge / cell division site / axoneme / cleavage furrow / protein polymerization / cilium assembly / enzyme regulator activity / cell projection / spindle microtubule / regulation of protein localization / neuron projection development / microtubule cytoskeleton / actin cytoskeleton / synaptic vesicle / myelin sheath / cell cortex / midbody / spermatogenesis / molecular adaptor activity / GTPase activity / synapse / GTP binding / perinuclear region of cytoplasm / cell surface / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Septin 2 / Septin-type guanine nucleotide-binding (G) domain / Septin / Septin-type guanine nucleotide-binding (G) domain profile. / Septin / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Septin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsSirajuddin, M. / Wittinghofer, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: GTP-induced conformational changes in septins and implications for function
Authors: Sirajuddin, M. / Farkasovsky, M. / Zent, E. / Wittinghofer, A.
History
DepositionJan 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ncs_dom_lim / 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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: Septin-2
B: Septin-2
C: Septin-2
D: Septin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,18012
Polymers126,9944
Non-polymers2,1868
Water1,856103
1
A: Septin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2953
Polymers31,7481
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Septin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2953
Polymers31,7481
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Septin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2953
Polymers31,7481
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Septin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2953
Polymers31,7481
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Septin-2
B: Septin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5906
Polymers63,4972
Non-polymers1,0934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-26 kcal/mol
Surface area25300 Å2
MethodPISA
6
C: Septin-2
D: Septin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5906
Polymers63,4972
Non-polymers1,0934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-29 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.980, 118.440, 190.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PHEPHESERSERAA36 - 564 - 24
211PHEPHESERSERBB36 - 564 - 24
121LEULEUPROPROAA97 - 10365 - 71
221LEULEUPROPROBB97 - 10365 - 71
131ILEILEILEILEAA118 - 12286 - 90
231ILEILEILEILEBB118 - 12286 - 90
141ASNASNHISHISAA144 - 158112 - 126
241ASNASNHISHISBB144 - 158112 - 126
151VALVALHISHISAA165 - 172133 - 140
251VALVALHISHISBB165 - 172133 - 140
161VALVALILEILEAA175 - 210143 - 178
261VALVALILEILEBB175 - 210143 - 178
171PHEPHESERSERAA237 - 242205 - 210
271PHEPHESERSERBB237 - 242205 - 210
181ARGARGPHEPHEAA254 - 273222 - 241
281ARGARGPHEPHEBB254 - 273222 - 241
191THRTHRTYRTYRAA278 - 296246 - 264
291THRTHRTYRTYRBB278 - 296246 - 264
112METMETSERSERAA41 - 469 - 14
212METMETSERSERCC41 - 469 - 14
122VALVALTYRTYRAA99 - 10567 - 73
222VALVALTYRTYRCC99 - 10567 - 73
132PHEPHETYRTYRAA115 - 12183 - 89
232PHEPHETYRTYRCC115 - 12183 - 89
142ASNASNSERSERAA144 - 154112 - 122
242ASNASNSERSERCC144 - 154112 - 122
152ASPASPTYRTYRAA164 - 211132 - 179
252ASPASPTYRTYRCC164 - 211132 - 179
162PHEPHESERSERAA237 - 242205 - 210
262PHEPHESERSERCC237 - 242205 - 210
113PHEPHESERSERAA38 - 516 - 19
213PHEPHESERSERDD38 - 516 - 19
123VALVALCYSCYSAA99 - 11167 - 79
223VALVALCYSCYSDD99 - 11167 - 79
133ILEILEPHEPHEAA122 - 12690 - 94
233ILEILEPHEPHEDD122 - 12690 - 94
143VALVALILEILEAA146 - 153114 - 121
243VALVALILEILEDD146 - 153114 - 121
153LEULEULYSLYSAA163 - 169131 - 137
253LEULEULYSLYSDD163 - 169131 - 137
163ASNASNTHRTHRAA176 - 186144 - 154
263ASNASNTHRTHRDD176 - 186144 - 154
173ILEILEHISHISAA208 - 212176 - 180
273ILEILEHISHISDD208 - 212176 - 180
183VALVALSERSERAA239 - 242207 - 210
283VALVALSERSERDD239 - 242207 - 210
193LEULEULEULEUAA276 - 280244 - 248
293LEULEULEULEUDD276 - 280244 - 248
1103LEULEUVALVALAA287 - 290255 - 258
2103LEULEUVALVALDD287 - 290255 - 258

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Septin-2 / Neural precursor cell expressed developmentally down-regulated protein 5 / NEDD-5


Mass: 31748.412 Da / Num. of mol.: 4 / Fragment: sequence database residues 33-306
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sept2, Nedd-5, Nedd5 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: P42208
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.2M Potassium Acetate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97906 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 25, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 33762 / Redundancy: 4.8 % / Rmerge(I) obs: 0.078 / Rsym value: 0.061
Reflection shellResolution: 2.9→2.974 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 4.81 / Num. unique all: 3240 / Rsym value: 0.371

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QA5

2qa5


Resolution: 2.9→19.97 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.861 / Occupancy max: 1 / Occupancy min: 1 / SU B: 33.538 / SU ML: 0.341 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1689 5 %RANDOM
Rwork0.247 ---
obs0.249 33760 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.55 Å2 / Biso mean: 31.273 Å2 / Biso min: 9.24 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å20 Å2
2---2.08 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8147 0 132 103 8382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228432
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.98411374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3695982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69423.686407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.871151576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2661566
X-RAY DIFFRACTIONr_chiral_restr0.0780.21276
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026174
X-RAY DIFFRACTIONr_nbd_refined0.2180.23742
X-RAY DIFFRACTIONr_nbtor_refined0.3120.25496
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2316
X-RAY DIFFRACTIONr_metal_ion_refined0.070.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.27
X-RAY DIFFRACTIONr_mcbond_it0.5191.55116
X-RAY DIFFRACTIONr_mcangle_it0.92128053
X-RAY DIFFRACTIONr_scbond_it0.83533716
X-RAY DIFFRACTIONr_scangle_it1.4494.53321
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
11098TIGHT POSITIONAL0.040.05
11098TIGHT THERMAL1.260.5
2686TIGHT POSITIONAL0.040.05
2686TIGHT THERMAL1.320.5
3578TIGHT POSITIONAL0.050.05
3578TIGHT THERMAL1.560.5
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 120 -
Rwork0.33 2280 -
all-2400 -
obs--100 %

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