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- PDB-1k8f: CRYSTAL STRUCTURE OF THE HUMAN C-TERMINAL CAP1-ADENYLYL CYCLASE A... -

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Basic information

Entry
Database: PDB / ID: 1k8f
TitleCRYSTAL STRUCTURE OF THE HUMAN C-TERMINAL CAP1-ADENYLYL CYCLASE ASSOCIATED PROTEIN
ComponentsADENYLYL CYCLASE-ASSOCIATED PROTEIN
KeywordsUNKNOWN FUNCTION / CAP / CAP1 / ADENYLYL CYCLASE ASSOCIATED PROTEIN / ACTIN BINDING / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


regulation of adenylate cyclase activity / ameboidal-type cell migration / neutrophil degranulation / Role of ABL in ROBO-SLIT signaling / actin polymerization or depolymerization / establishment or maintenance of cell polarity / cortical actin cytoskeleton / adenylate cyclase binding / activation of adenylate cyclase activity / receptor-mediated endocytosis ...regulation of adenylate cyclase activity / ameboidal-type cell migration / neutrophil degranulation / Role of ABL in ROBO-SLIT signaling / actin polymerization or depolymerization / establishment or maintenance of cell polarity / cortical actin cytoskeleton / adenylate cyclase binding / activation of adenylate cyclase activity / receptor-mediated endocytosis / cell morphogenesis / azurophil granule lumen / Platelet degranulation / actin binding / focal adhesion / Neutrophil degranulation / signal transduction / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Adenylyl cyclase-associated protein CAP1 / Adenylate cyclase-associated CAP, N-terminal / CAP, conserved site, N-terminal / CAP, conserved site, C-terminal / Adenylate cyclase-associated CAP, N-terminal domain superfamily / Adenylate cyclase associated (CAP) N terminal / CAP protein signature 1. / CAP protein signature 2. / Adenylate cyclase-associated CAP / Adenylate cyclase-associated CAP, C-terminal ...Adenylyl cyclase-associated protein CAP1 / Adenylate cyclase-associated CAP, N-terminal / CAP, conserved site, N-terminal / CAP, conserved site, C-terminal / Adenylate cyclase-associated CAP, N-terminal domain superfamily / Adenylate cyclase associated (CAP) N terminal / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPatskovsky, Y.V. / Chance, M. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: 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.
History
DepositionOct 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 25, 2012Group: Database references
Revision 1.4Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Aug 16, 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: ADENYLYL CYCLASE-ASSOCIATED PROTEIN
B: ADENYLYL CYCLASE-ASSOCIATED PROTEIN
C: ADENYLYL CYCLASE-ASSOCIATED PROTEIN
D: ADENYLYL CYCLASE-ASSOCIATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)69,4484
Polymers69,4484
Non-polymers00
Water0
1
A: ADENYLYL CYCLASE-ASSOCIATED PROTEIN
B: ADENYLYL CYCLASE-ASSOCIATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)34,7242
Polymers34,7242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-19 kcal/mol
Surface area14430 Å2
MethodPISA
2
C: ADENYLYL CYCLASE-ASSOCIATED PROTEIN
D: ADENYLYL CYCLASE-ASSOCIATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)34,7242
Polymers34,7242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-19 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.640, 83.120, 99.960
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
ADENYLYL CYCLASE-ASSOCIATED PROTEIN / CAP


Mass: 17361.912 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAP1 / Plasmid: PCRTOPO-NT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q01518

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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: 2.38 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, pH 8.5, 27.5% PEG4000, 0.2M NaOAc, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 83 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 16, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 16727 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 9.06 % / Rmerge(I) obs: 0.059 / Rsym value: 0.054 / Net I/σ(I): 20.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 6.3 / Rsym value: 0.154 / % possible all: 92.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K4Z

1k4z


Resolution: 2.8→10 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0.001 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.268 765 4.8 %RANDOM
Rwork0.232 ---
obs0.232 15935 93.3 %-
all-16727 --
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4864 0 0 0 4864
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.34
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d31.45
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.64
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.52.33
X-RAY DIFFRACTIONx_mcangle_it23.79
X-RAY DIFFRACTIONx_scbond_it24.02
X-RAY DIFFRACTIONx_scangle_it2.56.42
LS refinement shellResolution: 2.8→2.92 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.327 94 5.09 %
Rwork0.292 1846 -
obs--90.5 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO

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