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- PDB-3l8n: Crystal Structure of a domain of Brefeldin A-inhibited guanine nu... -

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Basic information

Entry
Database: PDB / ID: 3l8n
TitleCrystal Structure of a domain of Brefeldin A-inhibited guanine nucleotide-exchange protein 2 (BrefeldinA-inhibited GEP 2) from Homo sapiens (Human). Northeast Structural Genomics Consortium target id HR5562A
ComponentsBrefeldin A-inhibited guanine nucleotide-exchange protein 2
KeywordsNucleotide-binding protein / Metal-binding protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Guanine-nucleotide releasing factor / Phosphoprotein
Function / homology
Function and homology information


endomembrane system organization / symmetric synapse / receptor recycling / axonemal microtubule / Golgi to plasma membrane transport / endosome organization / GABA receptor binding / regulation of ARF protein signal transduction / myosin binding / protein kinase A regulatory subunit binding ...endomembrane system organization / symmetric synapse / receptor recycling / axonemal microtubule / Golgi to plasma membrane transport / endosome organization / GABA receptor binding / regulation of ARF protein signal transduction / myosin binding / protein kinase A regulatory subunit binding / exocytosis / Association of TriC/CCT with target proteins during biosynthesis / microtubule organizing center / asymmetric synapse / guanyl-nucleotide exchange factor activity / trans-Golgi network / GABA-ergic synapse / recycling endosome / positive regulation of tumor necrosis factor production / protein transport / presynapse / cytoplasmic vesicle / dendritic spine / intracellular signal transduction / Golgi membrane / centrosome / perinuclear region of cytoplasm / glutamatergic synapse / membrane / 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-like helical / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Brefeldin A-inhibited guanine nucleotide-exchange protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.86 Å
AuthorsSeetharaman, J. / Su, M. / Forouhar, F. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. ...Seetharaman, J. / Su, M. / Forouhar, F. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of a domain of Brefeldin A-inhibited guanine nucleotide-exchange protein 2 (BrefeldinA-inhibited GEP 2) from Homo sapiens (Human). Northeast Structural Genomics Consortium target id HR5562A
Authors: Seetharaman, J. / Su, M. / Forouhar, F. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionDec 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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 / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Brefeldin A-inhibited guanine nucleotide-exchange protein 2


Theoretical massNumber of molelcules
Total (without water)23,7891
Polymers23,7891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.929, 53.929, 75.711
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Brefeldin A-inhibited guanine nucleotide-exchange protein 2 / Brefeldin A-inhibited GEP 2


Mass: 23788.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARFGEF2, ARFGEP2, BIG2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6D5
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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG1000, sodium citrate, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.321
ReflectionResolution: 2.8→50 Å / Num. all: 13133 / Num. obs: 13133 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 79.4 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.071
Reflection shellResolution: 2.8→2.91 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.343 / Rsym value: 0.29 / % possible all: 99.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.86→17.65 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 306158.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED. The data is twined with twinning operator= -h,-k,l and twinning fraction= 0.321.
RfactorNum. reflection% reflectionSelection details
Rfree0.2901 914 9.3 %RANDOM
Rwork0.2362 ---
obs0.2362 9846 86.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.2813 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 74.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.23 Å20 Å20 Å2
2--4.23 Å20 Å2
3----8.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.6 Å
Luzzati d res low-5 Å
Luzzati sigma a1.35 Å0.98 Å
Refinement stepCycle: LAST / Resolution: 2.86→17.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 0 0 1300
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008509
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.53903
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 6
Num. reflection% reflection
Rfree79 9.1 %
Rwork792 -
obs-42.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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