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- PDB-2qnr: Human septin 2 in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 2qnr
TitleHuman septin 2 in complex with GDP
ComponentsSeptin-2
KeywordsCELL CYCLE / septin / Structural Genomics Consortium / SGC / mitosis / gdp / Cell division / GTP-binding / Nucleotide-binding / Phosphorylation
Function / homology
Function and homology information


sperm annulus / septin complex / photoreceptor connecting cilium / cytoskeleton-dependent cytokinesis / septin ring / regulation of exocytosis / non-motile cilium / ciliary membrane / smoothened signaling pathway / intercellular bridge ...sperm annulus / septin complex / photoreceptor connecting cilium / cytoskeleton-dependent cytokinesis / septin ring / regulation of exocytosis / non-motile cilium / ciliary membrane / smoothened signaling pathway / intercellular bridge / cell division site / axoneme / cleavage furrow / cilium assembly / Anchoring of the basal body to the plasma membrane / kinetochore / spindle / microtubule cytoskeleton / actin cytoskeleton / synaptic vesicle / midbody / spermatogenesis / molecular adaptor activity / cell differentiation / cadherin binding / GTPase activity / GTP binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Septin 2 / Septin-type guanine nucleotide-binding (G) domain / Septin / Septin-type guanine nucleotide-binding (G) domain profile. / Septin / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Septin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / sad / Resolution: 2.6 Å
AuthorsRabeh, W.M. / Nedyalkova, L. / Tempel, W. / Landry, R. / Crombet, L. / Kozieradzki, I. / Senisterra, G. / Vedadi, M. / Arrowsmith, C.H. / Edwards, A.M. ...Rabeh, W.M. / Nedyalkova, L. / Tempel, W. / Landry, R. / Crombet, L. / Kozieradzki, I. / Senisterra, G. / Vedadi, M. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human septin 2 in complex with GDP.
Authors: Rabeh, W.M. / Nedyalkova, L. / Tempel, W. / Landry, R. / Crombet, L. / Kozieradzki, I. / Senisterra, G. / Vedadi, M. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionJul 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Septin-2
B: Septin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9098
Polymers70,0222
Non-polymers8866
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.536, 52.295, 110.944
Angle α, β, γ (deg.)90.000, 132.480, 90.000
Int Tables number5
Space group name H-MC121
Detailsnot known

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Components

#1: Protein Septin-2 / Protein NEDD5


Mass: 35011.152 Da / Num. of mol.: 2 / Fragment: Residues 22-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT2, DIFF6, KIAA0158, NEDD5 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: Q15019
#2: Chemical ChemComp-GDP / GUANOSINE-5'-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-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically

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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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: PEG 3350, 0.2M Trilithium citrate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9777 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 22998 / % possible obs: 98.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.057 / Χ2: 1.86 / Net I/σ(I): 17.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.596.50.43521930.973195.4
2.59-2.697.10.37222511.02198.9
2.69-2.817.30.26322971.103198.9
2.81-2.967.30.17722831.19199.3
2.96-3.157.40.12123031.455199.3
3.15-3.397.40.08223081.73199.5
3.39-3.737.20.0723142.519199.2
3.73-4.267.40.05323162.519199.7
4.26-5.357.40.04423342.696199.7
5.35-22.9987.10.03323993.142199.5

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Phasing

PhasingMethod: sad

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RESOLVEphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.295 / WRfactor Rwork: 0.231 / SU B: 30.037 / SU ML: 0.29 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.491 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. Hydrogens have been added in the riding positions. 2. Coot, O, molprobity programs have also been used in the refinement. 3. Atomic B-factors shown are residuals from TLS refinement. 4. ...Details: 1. Hydrogens have been added in the riding positions. 2. Coot, O, molprobity programs have also been used in the refinement. 3. Atomic B-factors shown are residuals from TLS refinement. 4. CAVEAT: residues 84-89 in chain A and 74-90 in chain B could not be reliably assigned in the amino acid sequence and were modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1036 4.9 %thin shells
Rwork0.234 ---
all0.237 ---
obs-21100 97.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.672 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å2-2.21 Å2
2--0.94 Å20 Å2
3----3.05 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3515 0 60 0 3575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223632
X-RAY DIFFRACTIONr_bond_other_d0.0020.022413
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.9824921
X-RAY DIFFRACTIONr_angle_other_deg0.88935882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0625442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41223.487152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.61615612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2891524
X-RAY DIFFRACTIONr_chiral_restr0.0730.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023925
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02729
X-RAY DIFFRACTIONr_nbd_refined0.2250.2766
X-RAY DIFFRACTIONr_nbd_other0.1960.22426
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21757
X-RAY DIFFRACTIONr_nbtor_other0.0870.21986
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3410.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.21
X-RAY DIFFRACTIONr_mcbond_it2.43522325
X-RAY DIFFRACTIONr_mcbond_other0.5162908
X-RAY DIFFRACTIONr_mcangle_it3.43133620
X-RAY DIFFRACTIONr_scbond_it2.32421495
X-RAY DIFFRACTIONr_scangle_it3.27231301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.6660.4471360.3461366155896.406
2.666-2.73800.3081479150898.077
2.738-2.8160.3921190.2741334150196.802
2.816-2.9010.294240.2781393145997.121
2.901-2.9940.3371220.2661253140997.587
2.994-3.09600.2411330136597.436
3.096-3.210.326910.241166129896.841
3.21-3.33800.2461219127095.984
3.338-3.4820.347950.2531068123294.399
3.482-3.6460.344960.276964114892.334
3.646-3.83600.2671073111196.58
3.836-4.060.316610.218986107997.034
4.06-4.3270.224740.2913100398.405
4.327-4.65600.16590290699.559
4.656-5.0730.184740.17580788599.548
5.073-5.6270.243350.21474878599.745
5.627-6.4130.247240.25669071599.86
6.413-7.660.341530.24856061499.837
7.66-10.1160.37790.20849550699.605
10.116-200.244230.25431834798.271
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)
11.19340.3281-2.16721.3801-0.70297.76080.0373-0.11260.2150.17940.0448-0.0697-0.1816-0.0987-0.08210.29560.0341-0.03210.3727-0.07510.144459.92411.7998.029
21.94231.7211.6763.19582.87944.55250.04320.2101-0.0346-0.22750.0184-0.2062-0.10790.0148-0.06150.30320.04060.04070.40650.0350.077558.671-1.554-27.607
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 306
2X-RAY DIFFRACTION2B36 - 306

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