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- PDB-7eb6: Crystal structure of GTP-binding protein-like domain of AGAP1 -

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Basic information

Entry
Database: PDB / ID: 7eb6
TitleCrystal structure of GTP-binding protein-like domain of AGAP1
ComponentsArf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
KeywordsCELL ADHESION / AGAP1 / GTP-binding protein-like domain / leukemia
Function / homology
Function and homology information


GTPase activator activity / phospholipid binding / protein transport / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
: / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / small GTPase Rab1 family profile. / PH domain profile. / Pleckstrin homology domain. ...: / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / small GTPase Rab1 family profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Rab subfamily of small GTPases / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.014 Å
AuthorsCheng, N. / Zhang, H. / Zhang, S. / Ma, X. / Meng, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81970132, 81770142 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structure of the GTP-binding protein-like domain of AGAP1.
Authors: Cheng, N. / Zhang, H. / Zhang, S. / Ma, X. / Meng, G.
History
DepositionMar 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

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Assembly

Deposited unit
A: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)19,3551
Polymers19,3551
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.390, 100.390, 48.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1 / AGAP-1 / Centaurin-gamma-2 / Cnt-g2 / GTP-binding and GTPase-activating protein 1 / GGAP1


Mass: 19354.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGAP1, CENTG2, KIAA1099 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UPQ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / Details: PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.99 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.014→35.493 Å / Num. obs: 9136 / % possible obs: 99.57 % / Redundancy: 5.9 % / CC1/2: 0.949 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.7
Reflection shellResolution: 3.014→3.122 Å / Num. unique obs: 458 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IWR

2iwr


Resolution: 3.014→35.493 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2649 909 9.95 %
Rwork0.2327 8227 -
obs0.2359 9136 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.27 Å2 / Biso mean: 43.3223 Å2 / Biso min: 10.05 Å2
Refinement stepCycle: final / Resolution: 3.014→35.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 0 4 1312
Biso mean---16.91 -
Num. residues----165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0141-3.20280.36971480.317133698
3.2028-3.44990.32011540.2832137199
3.4499-3.79670.31681590.2613136499
3.7967-4.34530.23811590.213140799
4.3453-5.47140.21051410.1875137699
5.4714-35.4930.22391480.2098137398
Refinement TLS params.Method: refined / Origin x: 14.2952 Å / Origin y: -18.0363 Å / Origin z: -19.1304 Å
111213212223313233
T0.1201 Å20.0432 Å20.0488 Å2-0.0868 Å20.092 Å2--0.114 Å2
L1.2598 °20.0485 °2-0.2276 °2-0.948 °2-0.4411 °2--0.5759 °2
S-0.2152 Å °0.2597 Å °-0.5017 Å °0.4681 Å °-0.0886 Å °-0.2543 Å °-0.1918 Å °-0.0385 Å °-0.4059 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 69 through 233)

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