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- PDB-6mql: Crystal Structure of GTPase Domain of Human Septin 12 Mutant T89M -

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Basic information

Entry
Database: PDB / ID: 6mql
TitleCrystal Structure of GTPase Domain of Human Septin 12 Mutant T89M
ComponentsSeptin-12
KeywordsSTRUCTURAL PROTEIN / cytoskeleton component septin GTPase spermatogenesis
Function / homology
Function and homology information


sperm annulus / septin complex / cytoskeleton-dependent cytokinesis / septin ring / cell division site / cleavage furrow / stress fiber / phosphatidylinositol binding / spindle / GDP binding ...sperm annulus / septin complex / cytoskeleton-dependent cytokinesis / septin ring / cell division site / cleavage furrow / stress fiber / phosphatidylinositol binding / spindle / GDP binding / microtubule cytoskeleton / midbody / spermatogenesis / molecular adaptor activity / cell differentiation / GTPase activity / GTP binding / perinuclear region of cytoplasm / protein homodimerization activity / identical protein binding / nucleus
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-12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsCastro, D.K.S.V. / Pereira, H.M. / Brandao-Neto, J. / Ulian, A.P.U. / Garratt, R.C.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/15546-1 Brazil
Sao Paulo Research Foundation (FAPESP)2016/19734-2 Brazil
CitationJournal: To Be Published
Title: Crystal Structure of GTPase Domain of Human Septin 12
Authors: Castro, D.K.S.V. / Pereira, H.M. / Brandao-Neto, J. / Ulian, A.P.U. / Garratt, R.C.
History
DepositionOct 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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

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Assembly

Deposited unit
A: Septin-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5943
Polymers34,1261
Non-polymers4682
Water81145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Septin-12
hetero molecules

A: Septin-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1876
Polymers68,2522
Non-polymers9354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_856-x+3,y,-z+11
Buried area4120 Å2
ΔGint-37 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.920, 56.490, 70.290
Angle α, β, γ (deg.)90.000, 114.860, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Septin-12 /


Mass: 34126.195 Da / Num. of mol.: 1 / Mutation: T89M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT12 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q8IYM1
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.21 Å3/Da / Density % sol: 44.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% w/v PEG 4000, 20% v/v glycerol, 0.1 M bicine/Trizma base pH 8.5, 30mM of each: diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethyleneglycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.17→28.25 Å / Num. obs: 15878 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.995 / Rpim(I) all: 0.059 / Net I/σ(I): 8.7
Reflection shellResolution: 2.17→2.23 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1161 / CC1/2: 0.528 / Rpim(I) all: 0.488 / % possible all: 99.6

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MQ9

6mq9


Resolution: 2.17→28.245 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.64
RfactorNum. reflection% reflection
Rfree0.2387 737 4.64 %
Rwork0.214 --
obs0.2152 15874 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.11 Å2 / Biso mean: 55.9275 Å2 / Biso min: 28.67 Å2
Refinement stepCycle: final / Resolution: 2.17→28.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 29 45 2163
Biso mean--39.59 49.96 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022167
X-RAY DIFFRACTIONf_angle_d0.5582952
X-RAY DIFFRACTIONf_chiral_restr0.043339
X-RAY DIFFRACTIONf_plane_restr0.004381
X-RAY DIFFRACTIONf_dihedral_angle_d18.7881311
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1701-2.33760.35791460.304430063152
2.3376-2.57270.28451480.296229923140
2.5727-2.94460.32541340.25530393173
2.9446-3.70850.20691430.20230263169
3.7085-28.24740.21141660.180930743240
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)
18.73130.59312.1294.593.5495.987-0.1594-0.3230.755-0.2308-0.2390.4552-0.763-0.93150.23070.33390.07890.03860.4793-0.02090.444191.216137.935921.7815
25.2344-6.37516.97118.0009-8.35069.37970.3082-0.4483-0.7847-0.00830.14040.23350.4292-0.4113-0.4360.6463-0.0180.02930.46010.03350.6117104.848821.200329.17
38.75273.3855.43772.90922.55774.67320.3969-0.4841-0.37370.0313-0.08310.12140.356-0.4196-0.23590.3166-0.0404-0.0030.42520.04040.333986.34621.156511.4095
44.31921.08412.55992.47241.05314.5956-0.15480.6329-0.0075-0.26220.1773-0.0919-0.08450.5211-0.0130.2749-0.04550.03880.41770.01360.3123110.377232.98916.4669
53.2544-0.0678-0.30371.63740.56826.7319-0.33210.14690.6476-0.03950.12960.1733-0.904-0.02220.21160.519-0.0375-0.07210.33720.09270.5778103.559148.536518.7886
63.85444.7523.49279.03337.10827.1545-0.25880.30980.0988-0.41130.18310.0639-0.28230.21750.07050.2322-0.00530.00570.43850.06940.308795.164329.01657.5511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 112 )A48 - 112
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 126 )A113 - 126
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 159 )A127 - 159
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 231 )A160 - 231
5X-RAY DIFFRACTION5chain 'A' and (resid 232 through 282 )A232 - 282
6X-RAY DIFFRACTION6chain 'A' and (resid 283 through 318 )A283 - 318

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