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- PDB-1k4z: C-terminal Domain of Cyclase Associated Protein -

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Basic information

Entry
Database: PDB / ID: 1k4z
TitleC-terminal Domain of Cyclase Associated Protein
ComponentsAdenylyl Cyclase-Associated Protein
KeywordsMEMBRANE PROTEIN / right-handed parallel beta-helix / intertwined dimer / actin-binding / New York SGX Research Center for Structural Genomics / NYSGXRC / Structural Genomics / PSI / Protein Structure Initiative
Function / homology
Function and homology information


positive regulation of actin filament depolymerization / actin cortical patch / regulation of actin filament polymerization / actin filament severing / actin filament depolymerization / mating projection tip / positive regulation of Ras protein signal transduction / positive regulation of mitochondrial fission / adenylate cyclase binding / : ...positive regulation of actin filament depolymerization / actin cortical patch / regulation of actin filament polymerization / actin filament severing / actin filament depolymerization / mating projection tip / positive regulation of Ras protein signal transduction / positive regulation of mitochondrial fission / adenylate cyclase binding / : / Neutrophil degranulation / actin filament organization / actin binding / Ras protein signal transduction / identical protein binding / cytoplasm
Similarity search - Function
Adenylate cyclase-associated CAP, N-terminal / CAP, conserved site, N-terminal / CAP, conserved site, C-terminal / Adenylate cyclase-associated CAP, N-terminal domain superfamily / : / CAP N-terminal conserved motif / CAP, N-terminal domain / CAP protein signature 1. / CAP protein signature 2. / Adenylate cyclase-associated CAP ...Adenylate cyclase-associated CAP, N-terminal / CAP, conserved site, N-terminal / CAP, conserved site, C-terminal / Adenylate cyclase-associated CAP, N-terminal domain superfamily / : / CAP N-terminal conserved motif / CAP, N-terminal domain / CAP protein signature 1. / CAP protein signature 2. / Adenylate cyclase-associated CAP / Adenylate cyclase-associated CAP, C-terminal / Adenylate cyclase associated (CAP) C terminal / Pectate Lyase C-like - #70 / Adenylate cyclase-associated CAP, C-terminal superfamily / CARP motif / Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product. / C-CAP/cofactor C-like domain / C-CAP/cofactor C-like domain profile. / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / Pectate Lyase C-like / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Adenylyl cyclase-associated protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsRozwarski, D.A. / Fedorov, A.A. / Dodatko, T. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
Citation
Journal: Biochemistry / Year: 2004
Title: Crystal structure of the actin binding domain of the cyclase-associated protein
Authors: Dodatko, T. / Fedorov, A.A. / Grynberg, M. / Patskovsky, Y. / Rozwarski, D.A. / Jaroszewski, L. / Aronoff-Spencer, E. / Kondraskina, E. / Irving, T. / Godzik, A. / Almo, S.C.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Two Separate Functions Are Encoded by the Carboxyl-terminal Domains of the Yeast Cyclase-associated Protein and Its Mammalian Homologs. Dimerization and Actin Binding.
Authors: Zelicof, A. / Protopopov, V. / David, D. / Lin, X.Y. / Lusgarten, V. / Gerst, J.E.
History
DepositionOct 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
SupersessionNov 2, 2004ID: 1F5I
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Adenylyl Cyclase-Associated Protein
B: Adenylyl Cyclase-Associated Protein


Theoretical massNumber of molelcules
Total (without water)35,0812
Polymers35,0812
Non-polymers00
Water2,882160
1
A: Adenylyl Cyclase-Associated Protein

A: Adenylyl Cyclase-Associated Protein


Theoretical massNumber of molelcules
Total (without water)35,0812
Polymers35,0812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y+1/2,z1
Buried area2510 Å2
ΔGint-27 kcal/mol
Surface area15360 Å2
MethodPISA, PQS
2
B: Adenylyl Cyclase-Associated Protein

B: Adenylyl Cyclase-Associated Protein


Theoretical massNumber of molelcules
Total (without water)35,0812
Polymers35,0812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_655-x+3/2,y,-z1
Buried area2530 Å2
ΔGint-27 kcal/mol
Surface area15350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.520, 86.810, 160.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
DetailsThe biological assembly is an intertwined C-CAP dimer, which can be constructed using chain A and its symmetry partner generated by a crystallographic two-fold axis; or using chain B and its symmetry partner, generated by another crystallographic two-fold axis.

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Components

#1: Protein Adenylyl Cyclase-Associated Protein / CAP


Mass: 17540.641 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P17555
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
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: 2.827 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 4000, lithium sulfate, HEPES, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, sitting drop / pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MTris-HCl1reservoirpH8.5
227.5 %PEG40001reservoir
30.2 Msodium acetate1reservoir
412-24 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.04 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 30, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. all: 17249 / Num. obs: 17249 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 49.7
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 5 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 16.4 / Num. unique all: 2732 / % possible all: 92.9
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 10 Å / Num. obs: 17479 / % possible obs: 97.3 % / Num. measured all: 105428
Reflection shell
*PLUS
Lowest resolution: 2.38 Å / % possible obs: 91.1 % / Num. unique obs: 1564 / Num. measured obs: 7805 / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 18.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→9.99 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1721 10 %RANDOM
Rwork0.207 ---
all0.213 17249 --
obs0.213 17249 97.8 %-
Solvent computationSolvent model: flat model / Bsol: 44.52 Å2 / ksol: 0.429148 e/Å3
Displacement parametersBiso mean: 32.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.3→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 0 0 160 2600
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_dihedral_angle_d27.6
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_mcbond_it1.641.5
X-RAY DIFFRACTIONc_mcangle_it2.782
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_scangle_it3.472.5
Refine LS restraints NCSNCS model details: restraints
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 253 9.3 %
Rwork0.224 2479 -
obs-2732 92.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.63
X-RAY DIFFRACTIONc_mcbond_it1.641.5
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_mcangle_it2.782
X-RAY DIFFRACTIONc_scangle_it3.472.5
LS refinement shell
*PLUS
% reflection Rfree: 9.3 % / Rfactor Rwork: 0.224 / Rfactor obs: 0.224

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