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- PDB-5cb2: the structure of candida albicans Sey1p in complex with GMPPNP -

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Basic information

Entry
Database: PDB / ID: 5cb2
Titlethe structure of candida albicans Sey1p in complex with GMPPNP
ComponentsProtein SEY1
KeywordsHYDROLASE / ER / Membrance fusion / Dynamin / Sey1p
Function / homology
Function and homology information


hexose transmembrane transport / endoplasmic reticulum inheritance / endoplasmic reticulum membrane fusion / cortical endoplasmic reticulum / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
RHD3/Sey1 / Sey1/RHD3-like, three-helix bundle domain / Root hair defective 3 GTP-binding protein (RHD3) GTPase domain / Sey1 three-helix bundle domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Protein SEY1
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsYan, L. / Sun, S. / Wang, W. / Shi, J. / Hu, X. / Wang, S. / Rao, Z. / Hu, J. / Lou, Z.
Funding support China, 3items
OrganizationGrant numberCountry
China Postdoctoral Science Foundation2014M550713 China
973 Program2013CB911103 and 2014CB542802 China
National Natural Science Foundation81322023 China
CitationJournal: J.Cell Biol. / Year: 2015
Title: Structures of the yeast dynamin-like GTPase Sey1p provide insight into homotypic ER fusion
Authors: Yan, L. / Sun, S. / Wang, W. / Shi, J. / Hu, X. / Wang, S. / Su, D. / Rao, Z. / Hu, J. / Lou, Z.
History
DepositionJun 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein SEY1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6713
Polymers79,1241
Non-polymers5472
Water37821
1
A: Protein SEY1
hetero molecules

A: Protein SEY1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,3416
Polymers158,2482
Non-polymers1,0934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area7700 Å2
ΔGint-42 kcal/mol
Surface area65850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.566, 120.926, 190.455
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-813-

HOH

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Components

#1: Protein Protein SEY1


Mass: 79124.000 Da / Num. of mol.: 1 / Fragment: UNP residues 1-692
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: SEY1, NAG6, CaO19.2151, CaO19.9698 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9C0L9, dynamin GTPase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. SEQUENCE CONFLICTS D270G, A337T AND I479V ARE BASED ON BAB43823.1 ACCORDING TO DATABASE Q9C0L9 ...1. SEQUENCE CONFLICTS D270G, A337T AND I479V ARE BASED ON BAB43823.1 ACCORDING TO DATABASE Q9C0L9 (SEY1_CANAL). 2. THE CODON CUG (MRNA CUG CORRESPONDS TO CTG IN DNA) WILL ENCODE SER IN CANDIDA ALBICANS BUT LEU IN ESCHERICHIA COLI. SO 89S,221S,665S IN CANDIDA ALBICANS SEY1P(BAB43817) WILL BE TRANSLATED INTO LEU IN ESCHERICHIA COLI BL21.

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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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 120 Mm DL-Malic acid pH 7.0, 16% w/v PEG 3350, 20 mM Bicine pH 9.0, 400 mM Magnesium chloride hexahydrate, 6% D-(+)-Trehalose dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 19897 / % possible obs: 99.5 % / Redundancy: 6.9 % / Net I/σ(I): 27.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data processing
Cootmodel building
RefinementResolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.897 / SU B: 45.901 / SU ML: 0.412 / Cross valid method: THROUGHOUT / ESU R Free: 0.469 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29806 1015 5.1 %RANDOM
Rwork0.2596 ---
obs0.26156 18876 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.009 Å2
Baniso -1Baniso -2Baniso -3
1-8.07 Å20 Å2-0 Å2
2---3.53 Å20 Å2
3----4.54 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5303 0 33 21 5357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195426
X-RAY DIFFRACTIONr_bond_other_d0.0060.025180
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.9627338
X-RAY DIFFRACTIONr_angle_other_deg0.968311940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9575654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.92425.714273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.26415993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2991518
X-RAY DIFFRACTIONr_chiral_restr0.0980.2827
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026117
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021235
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.2437.5252622
X-RAY DIFFRACTIONr_mcbond_other6.2447.5222621
X-RAY DIFFRACTIONr_mcangle_it10.08211.2743274
X-RAY DIFFRACTIONr_mcangle_other10.0811.2773275
X-RAY DIFFRACTIONr_scbond_it5.3637.7862804
X-RAY DIFFRACTIONr_scbond_other5.3657.7922801
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.0711.5334062
X-RAY DIFFRACTIONr_long_range_B_refined13.99158.2496549
X-RAY DIFFRACTIONr_long_range_B_other13.99358.256549
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.901→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 69 -
Rwork0.383 1330 -
obs--95.69 %
Refinement TLS params.Method: refined / Origin x: -3.2169 Å / Origin y: 19.6358 Å / Origin z: 24.9527 Å
111213212223313233
T0.4094 Å2-0.0203 Å2-0.0038 Å2-0.1264 Å20.0453 Å2--0.0303 Å2
L0.0206 °20.0445 °20.1157 °2-0.1031 °20.2687 °2--0.8133 °2
S0.0513 Å °-0.0296 Å °-0.0058 Å °0.064 Å °-0.0661 Å °-0.0095 Å °0.2186 Å °-0.1651 Å °0.0148 Å °

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