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- PDB-4yqf: GTPase domain of Human Septin 9 -

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Basic information

Entry
Database: PDB / ID: 4yqf
TitleGTPase domain of Human Septin 9
ComponentsSeptin-9
KeywordsHYDROLASE / Cytoskeleton component. Septin GTPase
Function / homology
Function and homology information


septin complex / positive regulation of non-motile cilium assembly / cytoskeleton-dependent cytokinesis / septin ring / non-motile cilium / cell division site / axoneme / stress fiber / microtubule cytoskeleton / actin cytoskeleton ...septin complex / positive regulation of non-motile cilium assembly / cytoskeleton-dependent cytokinesis / septin ring / non-motile cilium / cell division site / axoneme / stress fiber / microtubule cytoskeleton / actin cytoskeleton / microtubule / molecular adaptor activity / cadherin binding / GTPase activity / GTP binding / perinuclear region of cytoplasm / cytoplasm
Similarity search - Function
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
GUANOSINE-5'-DIPHOSPHATE / Septin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsMatos, S.O. / Leonardo, D.A. / Macedo, J.N. / Pereira, H.M. / Araujo, A.P.U. / Garratt, R.C.
CitationJournal: To Be Published
Title: GTPase domain of Human Septin 9
Authors: Matos, S.O. / Leonardo, D.A. / Macedo, J.N. / Pereira, H.M. / Araujo, A.P.U. / Garratt, R.C.
History
DepositionMar 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Septin-9
A: Septin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2266
Polymers67,2912
Non-polymers9354
Water1,45981
1
B: Septin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1133
Polymers33,6461
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Septin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1133
Polymers33,6461
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.040, 77.523, 77.909
Angle α, β, γ (deg.)90.000, 105.810, 90.000
Int Tables number4
Space group name H-MP1211
DetailsMonomeric assembly confirmed by gel filtration

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Components

#1: Protein Septin-9 / / MLL septin-like fusion protein MSF-A / MLL septin-like fusion protein / Ovarian/Breast septin / ...MLL septin-like fusion protein MSF-A / MLL septin-like fusion protein / Ovarian/Breast septin / Ov/Br septin / Septin D1


Mass: 33645.578 Da / Num. of mol.: 2 / Fragment: UNP Residues 184-453
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT9, KIAA0991, MSF / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9UHD8
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.63 Å3/Da / Density % sol: 53.28 % / Description: Plates
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 24% PEG 1500, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 3, 2014
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.73→20 Å / Num. obs: 17271 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 44.95 Å2 / Rmerge F obs: 0.993 / Rmerge(I) obs: 0.122 / Rrim(I) all: 0.143 / Χ2: 0.956 / Net I/σ(I): 10.57 / Num. measured all: 61083
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.73-2.893.330.7490.6811.928683278626060.80793.5
2.89-3.090.8730.4572.989273260225950.53699.7
3.09-3.330.9410.2824.948718244324370.33299.8
3.33-3.630.9750.1738.037961222222190.20399.9
3.63-4.050.9880.1112.67360205920510.12999.6
4.05-4.640.9940.07118.356371179317840.08399.5
4.64-5.610.9960.0619.945625156915640.07199.7
5.61-7.630.9940.07217.654355123712260.08599.1
7.63-200.9990.02636.327378477890.03193.2

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Processing

Software
NameClassification
XDSdata scaling
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Unpublished high resolution model

Resolution: 2.73→19.726 Å / FOM work R set: 0.8086 / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 864 5 %Random selection
Rwork0.2076 16401 --
obs0.2096 17265 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.67 Å2 / Biso mean: 44.8 Å2 / Biso min: 9.06 Å2
Refinement stepCycle: final / Resolution: 2.73→19.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4007 0 58 81 4146
Biso mean--23.82 35.8 -
Num. residues----508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034142
X-RAY DIFFRACTIONf_angle_d0.8275618
X-RAY DIFFRACTIONf_chiral_restr0.032647
X-RAY DIFFRACTIONf_plane_restr0.003710
X-RAY DIFFRACTIONf_dihedral_angle_d14.7841518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7295-2.90.35461370.29222598X-RAY DIFFRACTION94
2.9-3.12310.28461440.26512729X-RAY DIFFRACTION100
3.1231-3.43590.27431450.23692759X-RAY DIFFRACTION100
3.4359-3.92970.26381450.19892748X-RAY DIFFRACTION100
3.9297-4.93810.20411450.17072763X-RAY DIFFRACTION100
4.9381-200.22961480.18942804X-RAY DIFFRACTION99
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)
15.72620.1958-1.85927.55890.29876.4015-0.20480.78140.0314-0.2368-0.08240.81010.041-0.19310.10740.4271-0.0836-0.03220.2414-0.05990.325626.9463-15.3946-53.4467
26.18070.643-1.29444.8559-0.03153.86170.030.0343-0.515-0.26040.1040.22580.90750.0051-0.14980.5843-0.1042-0.02830.2783-0.02150.319526.3181-22.5502-52.2877
36.0360.45875.42414.25551.17036.0457-0.51330.8304-0.0456-0.7871-0.4472-0.3481-0.55711.35450.43830.6323-0.00580.10510.46390.02430.481742.8384-10.459-46.729
45.0164-0.91821.64313.4241-1.16027.74630.06790.2150.1834-0.0019-0.1015-0.1396-0.17040.81480.08340.3272-0.03340.04920.3076-0.01230.273931.9912-12.5416-68.9549
51.9604-1.2144-0.13653.2139-0.83943.72070.08250.0620.3055-0.1746-0.17440.0098-0.5985-0.50740.08260.36060.0885-0.06210.35310.02380.374424.6465-2.8142-44.9637
68.06513.8473-1.25585.6398-0.2025.27310.27890.4528-0.9518-0.22380.1373-0.22191.0572-0.7769-0.18540.6169-0.0909-0.1650.4511-0.03230.503318.6782-19.7281-41.3619
76.11071.00770.34547.9609-2.2416.3628-0.103-0.1863-0.48420.33270.39190.18750.5479-1.2893-0.13540.3415-0.10690.03130.4617-0.03130.508714.3354-16.6159-42.4266
83.41240.3808-2.80424.5164-1.84738.60870.35290.1752-0.36920.19170.15980.0458-0.6645-0.794-0.39790.3933-0.0106-0.15020.42070.010.279126.7263-4.0811-66.4514
92.28470.21681.27691.1175-0.14223.2369-0.0308-0.01350.03680.0964-0.0099-0.0070.08670.13390.0360.23710.00920.0040.25440.02520.306143.1711-10.3739-20.0368
105.4459-3.6202-0.13134.4968-0.02053.68770.116-0.443-0.33270.3018-0.0260.11930.2192-0.2452-0.11960.3209-0.08240.00890.26610.06710.404928.8337-20.1989-16.1582
115.16431.88452.42483.07970.30651.97590.3347-0.5414-0.79040.3683-0.1596-0.46170.27910.375-0.13230.50740.12010.00420.4680.02940.39350.0441-14.6119-11.6235
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 21 through 35 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 36 through 87 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 88 through 101 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 102 through 134 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 135 through 219 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 220 through 239 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 240 through 269 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 270 through 290 )B0
9X-RAY DIFFRACTION9chain 'A' and (resid 21 through 206 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 207 through 257 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 258 through 290 )A0

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