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- PDB-1ifq: Sec22b N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 1ifq
TitleSec22b N-terminal domain
Componentsvesicle trafficking protein Sec22b
KeywordsPROTEIN TRANSPORT / FIVE-STRANDED ANTI-PARALLEL BETA SHEET / ALPHA/BETA 3-LAYER SANDWICH
Function / homology
Function and homology information


Cargo concentration in the ER / COPII-mediated vesicle transport / vesicle fusion with Golgi apparatus / COPI-coated vesicle / COPI-dependent Golgi-to-ER retrograde traffic / SNARE complex / negative regulation of autophagosome assembly / SNAP receptor activity / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / syntaxin binding ...Cargo concentration in the ER / COPII-mediated vesicle transport / vesicle fusion with Golgi apparatus / COPI-coated vesicle / COPI-dependent Golgi-to-ER retrograde traffic / SNARE complex / negative regulation of autophagosome assembly / SNAP receptor activity / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / syntaxin binding / ER-Phagosome pathway / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / ER to Golgi transport vesicle membrane / positive regulation of protein catabolic process / melanosome / protein transport / synaptic vesicle / Golgi membrane / endoplasmic reticulum membrane
Similarity search - Function
Vesicle-trafficking protein Sec22 / Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. ...Vesicle-trafficking protein Sec22 / Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Longin-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Vesicle-trafficking protein SEC22b
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsGonzalez Jr., L.C. / Weis, W.I. / Scheller, R.H.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: A novel snare N-terminal domain revealed by the crystal structure of Sec22b.
Authors: Gonzalez Jr., L.C. / Weis, W.I. / Scheller, R.H.
History
DepositionApr 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 20, 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 / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: vesicle trafficking protein Sec22b
B: vesicle trafficking protein Sec22b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2244
Polymers32,0402
Non-polymers1842
Water1,15364
1
A: vesicle trafficking protein Sec22b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1122
Polymers16,0201
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: vesicle trafficking protein Sec22b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1122
Polymers16,0201
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.244, 57.056, 99.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein vesicle trafficking protein Sec22b


Mass: 16019.801 Da / Num. of mol.: 2 / Fragment: N-Terminal Domain (residues 2-127)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pQE-9 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: O08547
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: PEG 1000, ammonium sulfate, sodium citrate, glycerol, beta-mercaptoethanol, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Details: drop contains protein and reservoir solution in a 1:1 ratio
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
227 %PEG10001reservoir
3100 mMammonium sulfate1reservoir
467 mMsodium citrate1reservoir
520 mMBME1reservoir
610 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.92537, 0.97929, 0.97945
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.925371
20.979291
30.979451
ReflectionResolution: 2.4→50 Å / Num. all: 21501 / Num. obs: 21210 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 50.3 Å2 / Limit h max: 21 / Limit h min: 0 / Limit k max: 24 / Limit k min: 0 / Limit l max: 42 / Limit l min: -43 / Observed criterion F max: 2462169.67 / Observed criterion F min: 1.715 / Rmerge(I) obs: 0.036 / Net I/σ(I): 31.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 5.3 / % possible all: 90.9
Reflection shell
*PLUS
% possible obs: 90.9 %

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→50 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1906 9.2 %random
Rwork0.231 ---
all-21501 --
obs-20615 95.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 57.9904 Å2 / ksol: 0.357432 e/Å3
Displacement parametersBiso max: 112.13 Å2 / Biso mean: 57.1 Å2 / Biso min: 30.71 Å2
Baniso -1Baniso -2Baniso -3
1-16.45 Å20 Å20 Å2
2--2.83 Å20 Å2
3----19.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.33 Å
Luzzati d res high-2.4
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 12 64 2029
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg21.8
X-RAY DIFFRACTIONx_torsion_impr_deg0.75
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.4-2.510.2992258.40.30522170.022686244290.9
2.51-2.640.3122248.20.32322840.0212716250892.3
2.64-2.810.2812278.50.2922790.0192664250694
2.81-3.020.2852479.20.28723560.0182683260397
3.02-3.330.2622278.40.25424180.0172693264598.2
3.33-3.810.26824590.25824180.0172708266398.3
3.81-4.80.2042338.70.19124220.0132677265599.2
4.8-500.18727810.40.19123150.0112683259396.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3sem_rep.paramgol.sol
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg

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