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- PDB-2yo0: Salmonella enterica SadA 1049-1304 fused to GCN4 adaptors (SadAK9-cfI) -

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Basic information

Entry
Database: PDB / ID: 2yo0
TitleSalmonella enterica SadA 1049-1304 fused to GCN4 adaptors (SadAK9-cfI)
ComponentsGENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN
KeywordsMEMBRANE PROTEIN / HANS MOTIF / YADA-LIKE HEAD / YLHEAD / HEAD INSERT MOTIF / HIM / TRIMERIC AUTOTRANSPORTER ADHESIN / TAA / CHIMERA
Function / homology
Function and homology information


protein localization to nuclear periphery / 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 / nitrogen catabolite activation of transcription from RNA polymerase II promoter / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II ...protein localization to nuclear periphery / 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 / nitrogen catabolite activation of transcription from RNA polymerase II promoter / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / cellular response to amino acid starvation / cell outer membrane / RNA polymerase II transcription regulator complex / : / protein transport / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / 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 / chromatin binding / negative regulation of transcription by RNA polymerase II / cell surface / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / ESPR domain / Extended Signal Peptide of Type V secretion system / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain ...Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / ESPR domain / Extended Signal Peptide of Type V secretion system / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pilin-like / Serralysin-like metalloprotease, C-terminal / Basic region leucine zipper / 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 / Mainly Beta
Similarity search - Domain/homology
General control transcription factor GCN4 / Autotransporter adhesin SadA
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHartmann, M.D. / Hernandez Alvarez, B. / Lupas, A.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Complete Fiber Structures of Complex Trimeric Autotransporter Adhesins Conserved in Enterobacteria.
Authors: Hartmann, M.D. / Grin, I. / Dunin-Horkawicz, S. / Deiss, S. / Linke, D. / Lupas, A.N. / Hernandez Alvarez, B.
History
DepositionOct 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0412
Polymers34,0051
Non-polymers351
Water362
1
A: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN
hetero molecules

A: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN
hetero molecules

A: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1236
Polymers102,0163
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area32400 Å2
ΔGint-209.8 kcal/mol
Surface area31930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.000, 54.000, 306.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-2337-

CL

21A-2001-

HOH

31A-2002-

HOH

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Components

#1: Protein GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN / AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN / AUTOTRANSPORTER ADHESIN FRAGMENT


Mass: 34005.398 Da / Num. of mol.: 1
Fragment: GCN4 ADAPTOR, RESIDUES 250-278, ADHESIN, RESIDUES 1049-1304
Mutation: YES
Source method: isolated from a genetically manipulated source
Details: N- AND C-TERMINAL IN-REGISTER FUSION TO GCN4 ADAPTORS
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast), (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03069, UniProt: Q8ZL64
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.6 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growDetails: 20% (V/V) BUTANEDIOL, 100 MM SODIUM ACETATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 7, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H,K,L10.571
11-H-K,K,-L20.429
ReflectionResolution: 2.8→37.2 Å / Num. obs: 12334 / % possible obs: 99.5 % / Redundancy: 3.25 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.59
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 3.22 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.07 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCM

1gcm


Resolution: 2.8→34.53 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.781 / SU B: 8.128 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29738 618 5 %RANDOM
Rwork0.22094 ---
obs0.22469 11712 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.145 Å2
Baniso -1Baniso -2Baniso -3
1-13.15 Å20 Å20 Å2
2--13.15 Å20 Å2
3----26.29 Å2
Refinement stepCycle: LAST / Resolution: 2.8→34.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 1 2 1989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211998
X-RAY DIFFRACTIONr_bond_other_d0.0010.021211
X-RAY DIFFRACTIONr_angle_refined_deg1.1371.9252715
X-RAY DIFFRACTIONr_angle_other_deg0.87733005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4325275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.12427.07989
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.16815323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.135157
X-RAY DIFFRACTIONr_chiral_restr0.0620.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022327
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02344
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4451.51355
X-RAY DIFFRACTIONr_mcbond_other0.0571.5575
X-RAY DIFFRACTIONr_mcangle_it0.81822165
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9673643
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6984.5550
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.803→2.875 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 46 -
Rwork0.211 826 -
obs--97.54 %

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