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- PDB-6mqb: Crystal Structure of GTPase Domain of Human Septin 12 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6mqb
TitleCrystal Structure of GTPase Domain of Human Septin 12 in complex with GMPPNP in Space Group C2221
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Septin-12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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: 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.D.V. / da Silva, S.M.O. / Pereira, H.D. / Macedo, J.N.A. / Leonardo, D.A. / Valadares, N.F. / Kumagai, P.S. / Brandao-Neto, J. / Araujo, A.P.U. / Garratt, R.C.
History
DepositionOct 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
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 1.3Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Septin-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6433
Polymers34,0961
Non-polymers5472
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, gel filtration
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)69,2856
Polymers68,1922
Non-polymers1,0934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5390 Å2
ΔGint-28 kcal/mol
Surface area23910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.020, 91.860, 151.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-590-

HOH

21A-592-

HOH

31A-598-

HOH

41A-599-

HOH

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Components

#1: Protein Septin-12 /


Mass: 34096.105 Da / Num. of mol.: 1
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): Roseta DE3 / References: UniProt: Q8IYM1
#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.: 100 / 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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.1 M MES/imidazole pH 6.5 and 20mM of each: sodium formate, ammonium acetate, trisodium citrate, sodium potassium l-tartrate, sodium oxamate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 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: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.12→45.93 Å / Num. obs: 16639 / % possible obs: 99.5 % / Redundancy: 5.3 % / Biso Wilson estimate: 38.63 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.063 / Net I/σ(I): 7.9
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.042 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6492 / CC1/2: 0.58 / Rpim(I) all: 0.48 / % possible all: 99.5

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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: 2.12→45.93 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.6
RfactorNum. reflection% reflection
Rfree0.2484 779 4.69 %
Rwork0.2 --
obs0.2022 16613 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.69 Å2 / Biso mean: 47.7229 Å2 / Biso min: 20.77 Å2
Refinement stepCycle: final / Resolution: 2.12→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2115 0 33 100 2248
Biso mean--28.95 47.98 -
Num. residues----267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022206
X-RAY DIFFRACTIONf_angle_d0.4773014
X-RAY DIFFRACTIONf_chiral_restr0.041346
X-RAY DIFFRACTIONf_plane_restr0.003387
X-RAY DIFFRACTIONf_dihedral_angle_d16.9951332
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.12-2.25280.31161240.275625862710
2.2528-2.42680.33481210.259826152736
2.4268-2.6710.29791210.252126042725
2.671-3.05740.28611540.229526042758
3.0574-3.85170.23961350.189826602795
3.8517-45.94080.1981240.164127652889
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)
14.52360.69291.90074.49062.46454.75340.04030.6189-0.2527-0.1780.1206-0.21080.17130.6894-0.16790.35110.04550.03660.38090.0140.33734.511-27.199820.0602
21.9566-0.40790.25961.91520.26313.18460.0360.430.0209-0.2041-0.0521-0.0409-0.10860.2630.00320.32810.02230.04240.39310.02630.35281.2111-15.05515.6685
31.51910.456-0.43142.1581-1.90113.25880.05990.18720.1793-0.20770.0570.12170.0594-0.1866-0.12770.26730.0355-0.00230.28610.01740.2924-5.8498-17.365921.7265
44.2972-1.17790.63335.0844-0.19094.88170.21170.3298-0.119-0.15-0.27060.33590.1385-0.55820.08630.2583-0.0298-0.02990.4080.00050.3645-15.5635-25.538826.7683
51.729-0.73031.12566.538-2.92894.28340.28430.1204-0.3177-0.65720.1290.46650.5754-0.0676-0.37350.18480.05370.05470.3136-0.06240.2576-6.0095-26.485817.4315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 92 )A48 - 92
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 145 )A93 - 145
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 200 )A146 - 200
4X-RAY DIFFRACTION4chain 'A' and (resid 201 through 254 )A201 - 254
5X-RAY DIFFRACTION5chain 'A' and (resid 255 through 319 )A255 - 319

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