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- PDB-4z51: High Resolution Human Septin 3 GTPase domain -

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Basic information

Entry
Database: PDB / ID: 4z51
TitleHigh Resolution Human Septin 3 GTPase domain
ComponentsNeuronal-specific septin-3
KeywordsHYDROLASE / GTPase / Septin / cytoskeleton
Function / homology
Function and homology information


presynaptic cytoskeleton / septin complex / septin ring / cytoskeleton-dependent cytokinesis / cell division site / microtubule cytoskeleton / presynapse / molecular adaptor activity / GTPase activity / GTP binding / identical protein binding
Similarity search - Function
Septin 3 / 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 / Neuronal-specific septin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å
AuthorsValadares, N.F. / Macedo, J.N. / Leonardo, D.A. / Brandao-Neto, J. / Pereira, H.M. / Matos, S.O. / Araujo, A.P.U. / Garratt, R.C.
CitationJournal: Iucrj / Year: 2020
Title: A complete compendium of crystal structures for the human SEPT3 subgroup reveals functional plasticity at a specific septin interface
Authors: Castro, D.K.S.V. / da Silva, S.M.O. / Pereira, H.M. / Macedo, J.N.A. / Leonardo, D.A. / Valadares, N.F. / Kumagai, P.S. / Brandao-Neto, J. / Araujo, A.P.U. / Garratt, R.C.
History
DepositionApr 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3May 13, 2020Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Sep 27, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuronal-specific septin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1663
Polymers31,6191
Non-polymers5472
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-11 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.280, 74.270, 79.210
Angle α, β, γ (deg.)90.000, 108.500, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-598-

HOH

DetailsMonomer confirmed by gel filtration

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Components

#1: Protein Neuronal-specific septin-3


Mass: 31619.217 Da / Num. of mol.: 1 / Fragment: UNP Residues 60-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT3, SEP3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UH03
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 50 mM magnesium acetate, 10mM Sodium Acetate, 15% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.86→75.12 Å / Num. obs: 23470 / % possible obs: 98.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 29.97 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-IDRejects% possible all
1.86-1.913.90.681099.7
8.32-75.123.70.0281095.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SOP

3sop


Resolution: 1.86→75.117 Å / FOM work R set: 0.8479 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 1205 5.13 %Random selection
Rwork0.1822 22264 --
obs0.1839 23469 98.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.01 Å2 / Biso mean: 41.61 Å2 / Biso min: 17.87 Å2
Refinement stepCycle: final / Resolution: 1.86→75.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 33 147 2181
Biso mean--22.95 44.43 -
Num. residues----253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042082
X-RAY DIFFRACTIONf_angle_d0.822825
X-RAY DIFFRACTIONf_chiral_restr0.031318
X-RAY DIFFRACTIONf_plane_restr0.004360
X-RAY DIFFRACTIONf_dihedral_angle_d14.112768
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.86-1.93450.25721320.22472465259799
1.9345-2.02260.27161420.221124562598100
2.0226-2.12920.24561320.21032509264199
2.1292-2.26260.24661400.20542447258798
2.2626-2.43730.23881040.19192462256699
2.4373-2.68260.23331300.19292463259398
2.6826-3.07080.24071410.19332464260599
3.0708-3.86890.20781540.17252468262299
3.8689-75.1780.18321300.16182530266098
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)
13.0559-0.08181.17783.625-0.82247.01710.070.32130.3725-0.1393-0.16610.28630.0478-0.380.05910.17930.02420.01350.3090.01270.31923.726437.487323.4328
25.7659-3.16315.54582.8058-3.34845.42020.7735-0.1826-0.2713-0.5837-0.1839-0.42091.12970.2108-0.53880.7140.0312-0.06260.3651-0.01160.466733.597121.273833.0068
34.48291.88571.86142.851.48778.12840.36540.4153-0.4137-0.1507-0.0811-0.19971.2447-0.2934-0.25030.6013-0.0371-0.0440.3977-0.04570.305224.485720.17914.7263
42.04590.98391.15821.11650.77483.41020.02540.2881-0.0504-0.12710.0312-0.00640.47640.1164-0.15270.30790.04650.01010.2460.00950.214134.002629.837120.1931
53.5903-0.1825-0.1253.57711.14482.58750.21140.75960.0447-0.0766-0.1268-0.1610.11440.3908-0.07170.26090.10350.05770.44540.06010.244847.250534.451719.6217
62.3228-1.50470.26183.77190.82742.5592-0.0010.2680.2122-0.37-0.12080.0377-0.29830.14360.15810.2133-0.00060.01370.25620.0710.334735.258248.039623.6357
71.3996-0.3909-0.23794.59624.18846.74210.26860.2450.3773-0.65330.0524-0.1576-0.7566-0.1596-0.0710.29790.05280.05860.28680.11640.375935.18848.159922.3115
84.2871.1664-1.01117.89242.46546.4418-0.38130.6589-0.3517-1.10820.30620.11410.60160.09020.09510.46710.1242-0.02930.50540.00310.232931.24624.42756.6246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 60 through 125 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 126 through 139 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 140 through 157 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 158 through 213 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 214 through 247 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 248 through 282 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 283 through 308 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 309 through 328 )A0

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