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- PDB-4oiy: Crystal structure of Sec7p catalytic domain -

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Basic information

Entry
Database: PDB / ID: 4oiy
TitleCrystal structure of Sec7p catalytic domain
ComponentsProtein transport protein SEC7
KeywordsPROTEIN TRANSPORT / sec7 domain / Guanine nucleotide exchange protein for ARF
Function / homology
Function and homology information


COPI-coated vesicle membrane / Intra-Golgi traffic / intra-Golgi vesicle-mediated transport / regulation of ARF protein signal transduction / cytoplasm protein quality control / Golgi-associated vesicle / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / guanyl-nucleotide exchange factor activity / trans-Golgi network ...COPI-coated vesicle membrane / Intra-Golgi traffic / intra-Golgi vesicle-mediated transport / regulation of ARF protein signal transduction / cytoplasm protein quality control / Golgi-associated vesicle / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / guanyl-nucleotide exchange factor activity / trans-Golgi network / ER to Golgi transport vesicle membrane / late endosome / protein transport / cytosol
Similarity search - Function
Mon2/Sec7/BIG1-like, HDS / Sec7/BIG1-like, C-terminal domain / Mon2/Sec7/BIG1-like, HDS / BIG2 C-terminal domain / Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, HUS domain / Mon2/Sec7/BIG1-like, HUS domain / Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 ...Mon2/Sec7/BIG1-like, HDS / Sec7/BIG1-like, C-terminal domain / Mon2/Sec7/BIG1-like, HDS / BIG2 C-terminal domain / Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, HUS domain / Mon2/Sec7/BIG1-like, HUS domain / Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 / Annexin V; domain 1 - #20 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Annexin V; domain 1 / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADP-ribosylation factor guanine nucleotide-exchange factor SEC7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsQiu, B. / Zhang, K. / Sun, F.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: C-terminal motif within Sec7 domain regulates guanine nucleotide exchange activity via tuning protein conformation
Authors: Qiu, B. / Zhang, K. / Wang, S.L. / Sun, F.
History
DepositionJan 20, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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: Protein transport protein SEC7
B: Protein transport protein SEC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8433
Polymers42,8192
Non-polymers241
Water3,927218
1
A: Protein transport protein SEC7


Theoretical massNumber of molelcules
Total (without water)21,4091
Polymers21,4091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein transport protein SEC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4342
Polymers21,4091
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.647, 68.961, 59.605
Angle α, β, γ (deg.)90.00, 106.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein transport protein SEC7


Mass: 21409.445 Da / Num. of mol.: 2 / Fragment: SEC7 DOMAIN, UNP residues 824-1010
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: s288c / Gene: SEC7 / Production host: Escherichia coli (E. coli) / References: UniProt: P11075
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEGMME550, 50mM MgCl2, 100mM Tris-Cl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97913 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 58905 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.8
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2927 / % possible all: 95.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R8M

1r8m


Resolution: 1.5→36.27 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.437 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23683 2747 5 %RANDOM
Rwork0.21112 ---
all0.21243 58905 --
obs0.21243 51944 90.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.1 Å2
2--0.12 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 1 218 3149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192985
X-RAY DIFFRACTIONr_bond_other_d0.0010.022886
X-RAY DIFFRACTIONr_angle_refined_deg1.0161.9744015
X-RAY DIFFRACTIONr_angle_other_deg0.70636659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.495369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76825.31145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84315553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8971514
X-RAY DIFFRACTIONr_chiral_restr0.0580.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023384
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02670
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 82 -
Rwork0.22 1423 -
obs--33.6 %

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