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- PDB-4nms: CFTR Associated Ligand (CAL)PDZ domain bound to peptide iCAL36(FL... -

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Basic information

Entry
Database: PDB / ID: 4nms
TitleCFTR Associated Ligand (CAL)PDZ domain bound to peptide iCAL36(FLB-K-1) (ANSRWPTS[4-fluorobenzoic-acyl-K]I)
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • iCAL36(FLB-K-1) peptide
Keywordsprotein transport/inhibitor / CAL / PIST / GOPC / FIG / CFTR / PDZ / PDZ-peptide / protein transport-inhibitor complex
Function / homology
Function and homology information


negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / trans-Golgi network transport vesicle / Golgi to plasma membrane transport / apical protein localization / RHOQ GTPase cycle / molecular sequestering activity / endoplasmic reticulum to Golgi vesicle-mediated transport ...negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / trans-Golgi network transport vesicle / Golgi to plasma membrane transport / apical protein localization / RHOQ GTPase cycle / molecular sequestering activity / endoplasmic reticulum to Golgi vesicle-mediated transport / protein transport / transmembrane transporter binding / postsynaptic density / Golgi membrane / lysosomal membrane / dendrite / Golgi apparatus / protein-containing complex / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Golgi-associated PDZ and coiled-coil motif-containing protein / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
iCAL36(FLB-K-1) peptide / Golgi-associated PDZ and coiled-coil motif-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAmacher, J.F. / Madden, D.R.
CitationJournal: Plos One / Year: 2014
Title: Chemically Modified Peptide Scaffolds Target the CFTR-Associated Ligand PDZ Domain.
Authors: Amacher, J.F. / Zhao, R. / Spaller, M.R. / Madden, D.R.
History
DepositionNov 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Golgi-associated PDZ and coiled-coil motif-containing protein
B: Golgi-associated PDZ and coiled-coil motif-containing protein
C: iCAL36(FLB-K-1) peptide
D: iCAL36(FLB-K-1) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4566
Polymers21,2724
Non-polymers1842
Water3,261181
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: iCAL36(FLB-K-1) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8204
Polymers10,6362
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-7 kcal/mol
Surface area5250 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: iCAL36(FLB-K-1) peptide


Theoretical massNumber of molelcules
Total (without water)10,6362
Polymers10,6362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-6 kcal/mol
Surface area5400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.275, 47.736, 97.776
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 Golgi-associated PDZ and coiled-coil motif-containing protein / CFTR-associated ligand / Fused in glioblastoma / PDZ protein interacting specifically with TC10 / PIST


Mass: 9353.722 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 284-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOPC, CAL, FIG / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9HD26
#2: Protein/peptide iCAL36(FLB-K-1) peptide


Type: Oligopeptide / Class: Inhibitor / Mass: 1282.400 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: peptide synthesis / References: iCAL36(FLB-K-1) peptide
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Details: peptide synthesis
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 1.99 Å3/Da / Density % sol: 38.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 33% (w/v) polyethylene glycol, 0.2 M sodium chloride, 0.1 M tris(hydroxymethyl)aminomethane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.8856 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 18, 2011
RadiationMonochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.7→19.5 Å / Num. all: 19370 / Num. obs: 19346 / % possible obs: 99.9 % / Observed criterion σ(F): 8.9 / Observed criterion σ(I): 16.33 / Rsym value: 0.089 / Net I/σ(I): 16.33
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.7-1.763.46217160199.9
1.77-1.95.23344739.6199.9
1.91-2.089.55316820.71100
2.09-2.3214.1286813.21100
2.33-2.6718.4725839.11100
2.68-3.2626.7422465.81100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4E34

4e34


Resolution: 1.7→19.537 Å / SU ML: 0.21 / Cross valid method: peptide density, not in model / σ(F): 2.01 / Phase error: 18.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 980 5.07 %In thin shells
Rwork0.1725 ---
obs0.1742 19345 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.718 Å2 / ksol: 0.414 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.624 Å20 Å2-0 Å2
2---0.8679 Å2-0 Å2
3----0.7562 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 12 181 1659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071502
X-RAY DIFFRACTIONf_angle_d1.12027
X-RAY DIFFRACTIONf_dihedral_angle_d15.25558
X-RAY DIFFRACTIONf_chiral_restr0.074230
X-RAY DIFFRACTIONf_plane_restr0.005260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.78960.26621470.22322551X-RAY DIFFRACTION100
1.7896-1.90160.24121470.18742573X-RAY DIFFRACTION100
1.9016-2.04830.2334980.15382620X-RAY DIFFRACTION100
2.0483-2.25420.19181470.15672587X-RAY DIFFRACTION100
2.2542-2.57970.19121470.17442614X-RAY DIFFRACTION100
2.5797-3.24770.20231470.16582640X-RAY DIFFRACTION100
3.2477-19.53810.19531470.17472780X-RAY DIFFRACTION100

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