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- PDB-5ca9: Structures of the candida albicans sey1p GTPase in complex with G... -

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Basic information

Entry
Database: PDB / ID: 5ca9
TitleStructures of the candida albicans sey1p GTPase in complex with GDPAlF4-
ComponentsProtein SEY1
KeywordsHYDROLASE / ER / Sey1p / membrance fusion / dynamin
Function / homology
Function and homology information


endoplasmic reticulum inheritance / hexose transmembrane transport / endoplasmic reticulum membrane fusion / cortical endoplasmic reticulum / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / endoplasmic reticulum membrane / GTP binding / 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
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Protein SEY1
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsYan, L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation81322023 China
973 Program2013CB911103 and 2014CB542802 China
Postdoctoral Science Foundation2014M550713 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 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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)79,6944
Polymers79,1241
Non-polymers5703
Water2,072115
1
A: Protein SEY1
hetero molecules

A: Protein SEY1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,3898
Polymers158,2482
Non-polymers1,1416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area8010 Å2
ΔGint-47 kcal/mol
Surface area65820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.272, 120.527, 190.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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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-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.77 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 160 mM Lithium sulfate monohydrate, 80 mM Tris pH 8.5, 20% w/v Polyethylene glycol 3,350, 40 mM Ammonium acetate, 20 mM Sodium citrate tribasic dihydrate pH 5.6, 6% w/v Polyethylene glycol ...Details: 160 mM Lithium sulfate monohydrate, 80 mM Tris pH 8.5, 20% w/v Polyethylene glycol 3,350, 40 mM Ammonium acetate, 20 mM Sodium citrate tribasic dihydrate pH 5.6, 6% w/v Polyethylene glycol 4,000, 20 mM spermidine

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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 8, 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: 21774 / % possible obs: 99 % / Redundancy: 10.28 % / Net I/σ(I): 43.9
Reflection shellResolution: 2.8→2.85 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data processing
PHENIXmodel building
RefinementResolution: 2.8→48.76 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.902 / SU B: 30.112 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27901 1121 5.1 %RANDOM
Rwork0.25277 ---
obs0.2541 20650 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.318 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0 Å20 Å2
2--0.48 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5303 0 34 115 5452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195426
X-RAY DIFFRACTIONr_bond_other_d0.0060.025179
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.9627337
X-RAY DIFFRACTIONr_angle_other_deg0.999311938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4255654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.14325.714273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.70715993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5671518
X-RAY DIFFRACTIONr_chiral_restr0.1070.2827
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026114
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021234
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_it5.9447.8682622
X-RAY DIFFRACTIONr_mcbond_other5.9447.8652621
X-RAY DIFFRACTIONr_mcangle_it9.59611.7883274
X-RAY DIFFRACTIONr_mcangle_other9.59511.7913275
X-RAY DIFFRACTIONr_scbond_it5.2367.9612804
X-RAY DIFFRACTIONr_scbond_other5.247.9742796
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.7811.8614051
X-RAY DIFFRACTIONr_long_range_B_refined14.39860.6396526
X-RAY DIFFRACTIONr_long_range_B_other14.39860.6396521
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.801→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.484 76 -
Rwork0.443 1332 -
obs--88.5 %
Refinement TLS params.Method: refined / Origin x: -3.0635 Å / Origin y: 19.4937 Å / Origin z: 24.972 Å
111213212223313233
T0.2508 Å2-0.0477 Å2-0.0123 Å2-0.0786 Å20.0347 Å2--0.0285 Å2
L0.0343 °20.0487 °20.1296 °2-0.0816 °20.1639 °2--0.8198 °2
S0.0563 Å °-0.0476 Å °-0.0152 Å °0.0395 Å °-0.0774 Å °-0.0317 Å °0.1716 Å °-0.1459 Å °0.0211 Å °

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