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- PDB-3i5c: Crystal structure of a fusion protein containing the leucine zipp... -

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Basic information

Entry
Database: PDB / ID: 3i5c
TitleCrystal structure of a fusion protein containing the leucine zipper of GCN4 and the GGDEF domain of WspR from Pseudomonas aeruginosa
ComponentsFusion of General control protein GCN4 and WSPR response regulator protein
KeywordsSIGNALING PROTEIN / c-di-GMP / GGDEF / leucine zipper
Function / homology
Function and homology information


diguanylate cyclase / negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase activity / protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation ...diguanylate cyclase / negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase activity / protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / cell adhesion involved in single-species biofilm formation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / phosphorelay signal transduction system / TFIID-class transcription factor complex binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / amino acid biosynthetic process / cellular response to nutrient levels / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / nucleotide binding / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / metal ion binding / plasma membrane
Similarity search - Function
: / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / : / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / GGDEF domain profile. / GGDEF domain / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. ...: / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / : / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / GGDEF domain profile. / GGDEF domain / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / General control transcription factor GCN4 / diguanylate cyclase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Pseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsNavarro, M.V.A.S. / De, N. / Sondermann, H.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Determinants for the activation and autoinhibition of the diguanylate cyclase response regulator WspR.
Authors: De, N. / Navarro, M.V. / Raghavan, R.V. / Sondermann, H.
History
DepositionJul 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion of General control protein GCN4 and WSPR response regulator protein
B: Fusion of General control protein GCN4 and WSPR response regulator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4357
Polymers45,6492
Non-polymers2,7865
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-10 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.813, 92.813, 133.693
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Fusion of General control protein GCN4 and WSPR response regulator protein


Mass: 22824.746 Da / Num. of mol.: 2 / Fragment: GCN4 leucine zipper fused with GGDEF domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Gene: PA3702, wspR, GCN4 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03069, UniProt: Q9HXT9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Magnesium formate dihydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9771 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 10, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9771 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. all: 43985 / Num. obs: 43941 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 18.1 % / Rsym value: 0.055 / Net I/σ(I): 55.1
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 4 / Rsym value: 0.606 / % possible all: 99.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→31.868 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.807 / SU ML: 1.7 / σ(F): 0.13 / Phase error: 25.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3119 7.33 %random
Rwork0.22 39421 --
obs0.223 42540 96.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.733 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso max: 113.09 Å2 / Biso mean: 38.862 Å2 / Biso min: 17.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.793 Å20 Å2-0 Å2
2--2.793 Å2-0 Å2
3----5.585 Å2
Refinement stepCycle: LAST / Resolution: 1.94→31.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3061 0 185 292 3538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063330
X-RAY DIFFRACTIONf_angle_d1.0464530
X-RAY DIFFRACTIONf_dihedral_angle_d17.2771316
X-RAY DIFFRACTIONf_chiral_restr0.067458
X-RAY DIFFRACTIONf_plane_restr0.016580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9401-1.97040.31731210.2451568X-RAY DIFFRACTION87
1.9704-2.00270.27411300.24631648X-RAY DIFFRACTION91
2.0027-2.03720.30691340.23961687X-RAY DIFFRACTION92
2.0372-2.07430.30571280.24061708X-RAY DIFFRACTION94
2.0743-2.11420.29221420.23311731X-RAY DIFFRACTION95
2.1142-2.15730.27491510.22251727X-RAY DIFFRACTION96
2.1573-2.20420.22851250.23371773X-RAY DIFFRACTION96
2.2042-2.25550.31421430.23471781X-RAY DIFFRACTION97
2.2555-2.31180.3011380.23191754X-RAY DIFFRACTION97
2.3118-2.37430.33091440.23261789X-RAY DIFFRACTION98
2.3743-2.44420.27121330.23061796X-RAY DIFFRACTION97
2.4442-2.5230.26631540.22441784X-RAY DIFFRACTION98
2.523-2.61320.28761230.2371832X-RAY DIFFRACTION99
2.6132-2.71770.32761460.24941824X-RAY DIFFRACTION99
2.7177-2.84140.27371460.23071822X-RAY DIFFRACTION99
2.8414-2.99110.29061380.24251849X-RAY DIFFRACTION99
2.9911-3.17830.26011480.23171845X-RAY DIFFRACTION100
3.1783-3.42340.25321400.21761864X-RAY DIFFRACTION100
3.4234-3.76750.24391710.20171846X-RAY DIFFRACTION100
3.7675-4.31150.21841670.1881865X-RAY DIFFRACTION100
4.3115-5.42760.20121450.18221931X-RAY DIFFRACTION100
5.4276-31.87270.23291520.21511997X-RAY DIFFRACTION98

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