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- PDB-1dcq: CRYSTAL STRUCTURE OF THE ARF-GAP DOMAIN AND ANKYRIN REPEATS OF PA... -

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Basic information

Entry
Database: PDB / ID: 1dcq
TitleCRYSTAL STRUCTURE OF THE ARF-GAP DOMAIN AND ANKYRIN REPEATS OF PAPBETA.
ComponentsPYK2-ASSOCIATED PROTEIN BETA
KeywordsMETAL BINDING PROTEIN / ZINC-BINDING MODULE / ANKYRIN REPEATS
Function / homology
Function and homology information


Golgi cisterna membrane / GTPase activator activity / metal ion binding / plasma membrane
Similarity search - Function
ASAP2, SH3 domain / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / Arf GTPase activating protein / 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 ...ASAP2, SH3 domain / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / Arf GTPase activating protein / 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 / Domain of unknown function DUF3447 / Annexin V; domain 1 / AH/BAR domain superfamily / Variant SH3 domain / Ankyrin repeat-containing domain / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Alpha Horseshoe / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsMandiyan, V. / Andreev, J. / Schlessinger, J. / Hubbard, S.R.
Citation
Journal: EMBO J. / Year: 1999
Title: Crystal structure of the ARF-GAP domain and ankyrin repeats of PYK2-associated protein beta.
Authors: Mandiyan, V. / Andreev, J. / Schlessinger, J. / Hubbard, S.R.
#1: Journal: Mol.Cell.Biol. / Year: 1999
Title: Identification of a new Pyk2 target protein with ARF-GAP activity.
Authors: Andreev, J. / Simon, J.P. / Sabatini, D.D. / Randazzo, P.A. / Schlessinger, J.
History
DepositionNov 5, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 14, 2016Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PYK2-ASSOCIATED PROTEIN BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9552
Polymers30,8891
Non-polymers651
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.935, 132.208, 59.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-85-

HOH

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Components

#1: Protein PYK2-ASSOCIATED PROTEIN BETA


Mass: 30889.277 Da / Num. of mol.: 1 / Fragment: ARF-GAP DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: BRAIN / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIG6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.37 Å3/Da / Density % sol: 44.8505 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 9.5
Details: PEG 4000, 0.2 M sodium acetate, 0.1 M Tris-HCl (pH 9.5), 15% ethylene glycol, VAPOR DIFFUSION, HANGING DROP
Crystal
*PLUS
Density % sol: 44.9 %
Crystal grow
*PLUS
Temperature: 20 ℃
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
230 %PEG40001reservoir
30.2 Msodium acetate1reservoir
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 14, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 78917 / Num. obs: 77917 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 24.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.119 / Num. unique all: 1656 / % possible all: 97.8
Reflection shell
*PLUS
% possible obs: 97.8 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1690 -RANDOM
Rwork0.213 ---
all0.23 16886 --
obs0.23 16886 96.5 %-
Solvent computationSolvent model: CNS / Bsol: 44.2 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.566 Å20 Å20 Å2
2--2.025 Å20 Å2
3---2.541 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 1 95 2169
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_impropers_deg0.9
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it2.242
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shellResolution: 2.1→2.18 Å
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4MISC.PARAM

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