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- PDB-3t5d: Crystal structure of Septin 7 in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 3t5d
TitleCrystal structure of Septin 7 in complex with GDP
ComponentsSeptin-7
KeywordsSIGNALING PROTEIN / GTP-binding protein / cytoskeleton
Function / homology
Function and homology information


regulation of embryonic cell shape / sperm annulus / septin complex / positive regulation of non-motile cilium assembly / cytoskeleton-dependent cytokinesis / septin ring / non-motile cilium / cell division site / axoneme / cleavage furrow ...regulation of embryonic cell shape / sperm annulus / septin complex / positive regulation of non-motile cilium assembly / cytoskeleton-dependent cytokinesis / septin ring / non-motile cilium / cell division site / axoneme / cleavage furrow / cilium assembly / stress fiber / MAPK6/MAPK4 signaling / spindle / kinetochore / microtubule cytoskeleton / midbody / spermatogenesis / cell differentiation / molecular adaptor activity / cadherin binding / GTPase activity / GTP binding / structural molecule activity / extracellular exosome / identical protein binding / nucleus / cytosol
Similarity search - Function
Septin 7 / 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-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsZent, E. / Wittinghofer, A.
CitationJournal: Biol.Chem. / Year: 2011
Title: Structural and biochemical properties of Sept7, a unique septin required for filament formation.
Authors: Zent, E. / Vetter, I. / Wittinghofer, A.
History
DepositionJul 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Septin-7
C: Septin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5864
Polymers62,7002
Non-polymers8862
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-17 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.363, 82.363, 210.598
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 2 / Auth seq-ID: 30 - 295 / Label seq-ID: 7 - 272

Dom-IDAuth asym-IDLabel asym-ID
1CB
2AA

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Components

#1: Protein Septin-7 / / CDC10 protein homolog


Mass: 31349.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT7, CDC10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16181
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.29 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.2M sodium chlorid, 1.1M ammonium sulfate, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99986 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 3.3→71.25 Å / Num. all: 12190 / Num. obs: 12079 / % possible obs: 99.1 % / Redundancy: 8.9 %
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 3.85 / Num. unique all: 1007 / Rsym value: 0.596 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PRODCdata collection
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→71.25 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.86 / SU B: 86.942 / SU ML: 0.653 / Cross valid method: THROUGHOUT / ESU R Free: 0.619 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31826 581 4.8 %RANDOM
Rwork0.28536 ---
obs0.28696 11498 99.28 %-
all-12079 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.02 Å2
Baniso -1Baniso -2Baniso -3
1--6.8 Å2-3.4 Å20 Å2
2---6.8 Å20 Å2
3---10.21 Å2
Refinement stepCycle: LAST / Resolution: 3.3→71.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3783 0 56 2 3841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223904
X-RAY DIFFRACTIONr_angle_refined_deg0.9121.9855270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0425457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96924.728184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22215736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0821524
X-RAY DIFFRACTIONr_chiral_restr0.0560.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022845
X-RAY DIFFRACTIONr_nbd_refined0.1650.21715
X-RAY DIFFRACTIONr_nbtor_refined0.2940.22624
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2117
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.26
X-RAY DIFFRACTIONr_mcbond_it0.3791.52425
X-RAY DIFFRACTIONr_mcangle_it0.68223774
X-RAY DIFFRACTIONr_scbond_it0.07931710
X-RAY DIFFRACTIONr_scangle_it0.1294.51496
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
C912tight positional0.010.05
A939medium positional0.130.5
C912tight thermal00.5
A939medium thermal0.032
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 42 -
Rwork0.358 817 -
obs--98.96 %

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