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- PDB-5irr: Crystal structure of Septin GTPase domain from Chlamydomonas rein... -

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Basic information

Entry
Database: PDB / ID: 5irr
TitleCrystal structure of Septin GTPase domain from Chlamydomonas reinhardtii
ComponentsSeptin-like protein
KeywordsHYDROLASE / Septin / GTPase domain
Function / homology
Function and homology information


septin complex / septin ring / cytoskeleton-dependent cytokinesis / cell division site / intracellular protein localization / microtubule cytoskeleton / molecular adaptor activity / GTPase activity / GTP binding / metal ion binding
Similarity search - Function
Septin-type guanine nucleotide-binding (G) domain / Septin / Septin-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Uncharacterized protein
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.04 Å
AuthorsPinto, A.P.A. / Pereira, H.M. / Navarro, M.V.A.S. / Brandao-Neto, J. / Garratt, R.C. / Araujo, A.P.U.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2011/10152-7 Brazil
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Filaments and fingers: Novel structural aspects of the single septin from Chlamydomonas reinhardtii.
Authors: Pinto, A.P.A. / Pereira, H.M. / Zeraik, A.E. / Ciol, H. / Ferreira, F.M. / Brandao-Neto, J. / DeMarco, R. / Navarro, M.V.A.S. / Risi, C. / Galkin, V.E. / Garratt, R.C. / Araujo, A.P.U.
History
DepositionMar 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.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.value / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Septin-like protein
B: Septin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2526
Polymers72,1252
Non-polymers1,1274
Water6,125340
1
A: Septin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6263
Polymers36,0621
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Septin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6263
Polymers36,0621
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.580, 39.410, 130.900
Angle α, β, γ (deg.)90.000, 118.500, 90.000
Int Tables number5
Space group name H-MC121
DetailsMonomer confirmed by gel filtration

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Components

#1: Protein Septin-like protein


Mass: 36062.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: SEP1, CHLREDRAFT_148151 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Variant (production host): rosetta / References: UniProt: A8IYS5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.57 % / Description: thick plates
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD; 30mM of each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate; 10mM bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.04→43.63 Å / Num. obs: 49936 / % possible obs: 97.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 32.48 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.04-2.093.90.729195.9
9.12-43.633.90.04198

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
xia2data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.04→43.628 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.55
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 2460 4.93 %Random selection
Rwork0.1946 ---
obs0.1964 49930 96.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.99 Å2 / Biso mean: 43.9287 Å2 / Biso min: 17.14 Å2
Refinement stepCycle: final / Resolution: 2.04→43.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4507 0 66 340 4913
Biso mean--27.07 47.15 -
Num. residues----559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034715
X-RAY DIFFRACTIONf_angle_d0.6396428
X-RAY DIFFRACTIONf_chiral_restr0.046706
X-RAY DIFFRACTIONf_plane_restr0.004813
X-RAY DIFFRACTIONf_dihedral_angle_d14.1642852
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.04-2.07920.31861470.30782582272996
2.0792-2.12170.30321100.28812388249889
2.1217-2.16780.31431360.2682595273195
2.1678-2.21820.26491400.24792624276497
2.2182-2.27370.30181410.24892639278099
2.2737-2.33520.25341320.23342640277297
2.3352-2.40390.28361350.22462655279099
2.4039-2.48150.23661300.21692699282998
2.4815-2.57020.23941310.21252651278299
2.5702-2.67310.2491450.21142684282999
2.6731-2.79470.24251340.20312717285199
2.7947-2.9420.23931340.19582632276698
2.942-3.12630.20141330.19342385251888
3.1263-3.36760.22291380.19312685282399
3.3676-3.70630.20391510.171227182869100
3.7063-4.24220.20651390.15732737287699
4.2422-5.34320.19051340.15942747288198
5.3432-43.63750.24991500.18862692284294
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)
13.14310.4312-2.49212.09610.53365.7320.07420.29430.552-0.07960.1092-0.0358-0.44880.1469-0.13240.1948-0.0053-0.02750.210.04450.315337.202546.440359.4362
26.67990.9708-4.40184.5243-1.44223.09340.1360.5960.6657-0.16530.08590.1374-0.6533-0.3769-0.23320.2297-0.0166-0.08080.37990.06280.315523.891242.985950.4943
32.2346-0.07711.02771.21930.33553.5277-0.00550.18050.04170.08410.06630.02860.08160.1789-0.06970.22250.0402-0.01290.1918-0.03530.238929.781234.759163.7706
48.7441.81466.44375.07962.15935.59940.5299-0.2849-0.87140.51320.18030.00981.0434-0.1507-0.52790.35630.0788-0.01260.204-0.03080.230833.397524.048975.3351
52.4662-0.4892-0.37072.0010.17872.6351-0.35410.6673-1.3572-0.16330.18130.06680.4141-0.10680.23910.37080.0871-0.00040.2892-0.0790.406631.680224.496260.458
66.57033.065-1.70885.3795-3.76453.3364-0.24820.1846-0.72190.12650.1353-0.41970.87090.31210.01750.26450.1238-0.05950.3053-0.03240.24541.578930.107769.9844
76.7217.2044-4.94737.8345-5.42593.87350.5265-0.76480.83290.0915-0.2933-1.3677-0.05860.96230.00150.3063-0.07980.15630.5142-0.18280.683154.590149.117676.0129
82.29480.35892.52670.84570.53136.44260.10320.3302-0.0752-0.18280.142-0.10190.2180.5238-0.29190.20220.00180.02260.1975-0.00620.219440.314136.10562.1627
90.99120.6464-0.0123.1679-3.51558.54410.1229-0.4665-0.07010.3130.13810.1548-0.3058-1.0018-0.16370.2172-0.00950.00510.47660.0450.269210.790133.3334105.0259
105.98571.0321-0.83735.48011.17523.58850.2176-0.2767-0.80180.3784-0.07020.181.1492-0.1005-0.23740.46230.0005-0.06660.19340.00050.336521.153526.826690.9534
112.7235-0.5467-2.78132.5090.30932.6594-0.0322-0.2842-0.24080.18320.15590.04020.6263-0.1493-0.10120.2303-0.0115-0.01780.27420.05670.227614.698330.809199.7031
127.47341.8943-5.88417.1243-1.98968.50050.0123-0.494-0.63750.0870.11910.40360.6907-1.0954-0.10590.2661-0.0689-0.0450.60550.09190.37961.957732.53690.6727
133.41690.01840.76971.66250.07351.84260.05-0.22150.1682-0.05350.05920.0187-0.0093-0.2068-0.0930.24030.0158-0.0050.2123-0.0450.278316.941741.559187.7752
145.1091-3.98931.72567.29321.10855.1442-0.22680.29141.1973-0.06660.1762-0.1813-0.34250.1940.06390.2487-0.01090.04620.149-0.06790.311827.941351.908785.3196
153.8171-0.69323.87392.3295-0.5787.6208-0.2357-0.40940.37580.25490.02850.089-1.0416-0.57250.30460.36990.0497-0.00660.2718-0.11150.336715.048451.670592.4638
164.67141.37941.07924.6463-2.63617.070.0613-0.44760.8720.29250.0348-0.1334-0.964-0.0604-0.17010.3045-0.0018-0.03370.2772-0.08010.291927.949345.89595.0828
173.5084-0.86182.95526.2971-5.19015.77480.3579-0.517-0.37190.98530.0151-0.2090.62080.8698-0.40580.65990.1995-0.09570.53520.00760.2940.336326.6433102.5039
183.6779-0.271-0.89420.99150.0273.09480.1843-0.57430.16140.2768-0.00090.1728-0.2407-0.2285-0.16770.31390.06370.0340.2346-0.02610.237621.958639.578998.3748
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 104 through 188 )B19 - 103
2X-RAY DIFFRACTION2chain 'B' and (resid 189 through 213 )B104 - 128
3X-RAY DIFFRACTION3chain 'B' and (resid 214 through 268 )B129 - 183
4X-RAY DIFFRACTION4chain 'B' and (resid 269 through 284 )B184 - 199
5X-RAY DIFFRACTION5chain 'B' and (resid 285 through 307 )B200 - 222
6X-RAY DIFFRACTION6chain 'B' and (resid 308 through 327 )B223 - 242
7X-RAY DIFFRACTION7chain 'B' and (resid 328 through 342 )B243 - 257
8X-RAY DIFFRACTION8chain 'B' and (resid 343 through 392 )B258 - 307
9X-RAY DIFFRACTION9chain 'A' and (resid 105 through 117 )A20 - 32
10X-RAY DIFFRACTION10chain 'A' and (resid 118 through 154 )A33 - 69
11X-RAY DIFFRACTION11chain 'A' and (resid 155 through 188 )A70 - 103
12X-RAY DIFFRACTION12chain 'A' and (resid 189 through 213 )A104 - 128
13X-RAY DIFFRACTION13chain 'A' and (resid 214 through 268 )A129 - 183
14X-RAY DIFFRACTION14chain 'A' and (resid 269 through 284 )A184 - 199
15X-RAY DIFFRACTION15chain 'A' and (resid 285 through 307 )A200 - 222
16X-RAY DIFFRACTION16chain 'A' and (resid 308 through 327 )A223 - 242
17X-RAY DIFFRACTION17chain 'A' and (resid 328 through 342 )A243 - 257
18X-RAY DIFFRACTION18chain 'A' and (resid 343 through 390 )A258 - 305

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