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- PDB-5nlv: Brag2 Sec7-PH (390-763) -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5nlv
TitleBrag2 Sec7-PH (390-763)
ComponentsIQ motif and SEC7 domain-containing protein 1
KeywordsHYDROLASE / small GTPase
Function / homology
Function and homology information


positive regulation of keratinocyte migration / dendritic spine development / positive regulation of focal adhesion disassembly / regulation of ARF protein signal transduction / guanyl-nucleotide exchange factor activity / synaptic vesicle / actin cytoskeleton organization / postsynaptic density / intracellular membrane-bounded organelle / lipid binding ...positive regulation of keratinocyte migration / dendritic spine development / positive regulation of focal adhesion disassembly / regulation of ARF protein signal transduction / guanyl-nucleotide exchange factor activity / synaptic vesicle / actin cytoskeleton organization / postsynaptic density / intracellular membrane-bounded organelle / lipid binding / nucleolus / membrane
Similarity search - Function
IQ motif and SEC7 domain-containing protein, PH domain / PH domain / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / IQ motif profile. / IQ motif, EF-hand binding site ...IQ motif and SEC7 domain-containing protein, PH domain / PH domain / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / IQ motif profile. / IQ motif, EF-hand binding site / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
IQ motif and SEC7 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNawrotek, A. / Cherfils, J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Multiple interactions between an Arf/GEF complex and charged lipids determine activation kinetics on the membrane.
Authors: Karandur, D. / Nawrotek, A. / Kuriyan, J. / Cherfils, J.
History
DepositionApr 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IQ motif and SEC7 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)47,4631
Polymers47,4631
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.434, 57.556, 75.262
Angle α, β, γ (deg.)90.00, 97.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein IQ motif and SEC7 domain-containing protein 1 / ADP-ribosylation factors guanine nucleotide-exchange protein 100 / ADP-ribosylation factors guanine ...ADP-ribosylation factors guanine nucleotide-exchange protein 100 / ADP-ribosylation factors guanine nucleotide-exchange protein 2 / Brefeldin-resistant Arf-GEF 2 protein / BRAG2


Mass: 47462.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IQSEC1, ARFGEP100, BRAG2, KIAA0763 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6DN90
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3 Å3/Da / Density % sol: 58.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 15% PEG3350, 300mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.4→18.94 Å / Num. obs: 19122 / % possible obs: 99.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 77.79 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.04 / Rsym value: 0.067 / Net I/σ(I): 13.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.1 / CC1/2: 0.733 / Rpim(I) all: 1.06 / Rsym value: 1.54 / % possible all: 97.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C0A chain E

5c0a


Resolution: 2.4→18.92 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.894 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.376 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.367 / SU Rfree Blow DPI: 0.242 / SU Rfree Cruickshank DPI: 0.247
RfactorNum. reflection% reflectionSelection details
Rfree0.259 939 4.97 %RANDOM
Rwork0.24 ---
obs0.241 18912 98.7 %-
Displacement parametersBiso mean: 90.81 Å2
Baniso -1Baniso -2Baniso -3
1-27.6491 Å20 Å2-13.3975 Å2
2---27.9487 Å20 Å2
3---0.2996 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: 1 / Resolution: 2.4→18.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2855 0 20 88 2963
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092946HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.043957HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1098SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes83HARMONIC2
X-RAY DIFFRACTIONt_gen_planes418HARMONIC5
X-RAY DIFFRACTIONt_it2946HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.04
X-RAY DIFFRACTIONt_other_torsion19.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion364SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3660SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.53 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.37 120 4.47 %
Rwork0.335 2564 -
all0.337 2684 -
obs--96.8 %
Refinement TLS params.Method: refined / Origin x: -26.3462 Å / Origin y: -17.6823 Å / Origin z: 21.5816 Å
111213212223313233
T-0.0108 Å20.0319 Å20.0098 Å2-0.0034 Å20.0086 Å2--0.001 Å2
L0.327 °2-0.6836 °2-0.2667 °2-0.338 °2-0.1811 °2--0.352 °2
S0.001 Å °0.0038 Å °-0.0005 Å °0.0097 Å °-0.01 Å °0.0149 Å °0.0032 Å °-0.0005 Å °0.009 Å °
Refinement TLS groupSelection details: { A|* }

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