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- PDB-5nly: Brag2 Sec7-PH (390-763), P212121 -

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Basic information

Entry
Database: PDB / ID: 5nly
TitleBrag2 Sec7-PH (390-763), P212121
Components(IQ motif and SEC7 domain-containing protein 1) x 2
KeywordsHYDROLASE / small GTPase
Function / homology
Function and homology information


regulation of ARF protein signal transduction / dendritic spine development / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / guanyl-nucleotide exchange factor activity / synaptic vesicle / actin cytoskeleton organization / postsynaptic density / intracellular membrane-bounded organelle / lipid binding ...regulation of ARF protein signal transduction / dendritic spine development / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / 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. / Pleckstrin homology domain. ...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. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / IQ motif and SEC7 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
B: IQ motif and SEC7 domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5653
Polymers95,4702
Non-polymers951
Water7,584421
1
A: IQ motif and SEC7 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)47,6971
Polymers47,6971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: IQ motif and SEC7 domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8682
Polymers47,7731
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.893, 66.039, 206.880
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 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: 47697.031 Da / Num. of mol.: 1 / Fragment: UNP residues 512-885
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: 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: 47773.152 Da / Num. of mol.: 1 / Fragment: UNP residues 512-885
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
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 15% PEG20000, O.1M Tris pH=8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.872899 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.872899 Å / Relative weight: 1
ReflectionResolution: 2→28.99 Å / Num. obs: 60129 / % possible obs: 99.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 29.39 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.05 / Rsym value: 0.13 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 22564 / CC1/2: 0.439 / Rpim(I) all: 0.86 / Rsym value: 1.26

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Processing

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

5nlv


Resolution: 2→28.99 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.915 / Rfactor Rfree error: 0.01 / SU R Cruickshank DPI: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.183 / SU Rfree Blow DPI: 0.152 / SU Rfree Cruickshank DPI: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2881 4.8 %RANDOM
Rwork0.208 ---
obs0.209 60012 99.9 %-
Displacement parametersBiso mean: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.2501 Å20 Å20 Å2
2--4.8037 Å20 Å2
3----4.5536 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: 1 / Resolution: 2→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5737 0 95 421 6253
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01211905HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2321577HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2662SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes172HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1688HARMONIC5
X-RAY DIFFRACTIONt_it11905HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.55
X-RAY DIFFRACTIONt_other_torsion14.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion733SEMIHARMONIC5
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_contact13510SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 187 4.35 %
Rwork0.227 4114 -
all0.228 4301 -
obs--99.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10-0.3013-0.06070.24560.003900.0003-0.0077-0.0038-0.0048-0.0028-0.0105-0.0099-0.0180.00250.0097-0.0016-0.0005-0.01340.00360.005511.27160.5969-42.1732
20.4010.18630.57200.08740.33780.0005-0.01170.0055-0.01160.0041-0.00160.0106-0.0079-0.0046-0.0152-0.0009-0.00710.0054-0.0177-0.003932.549829.0611-10.0506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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