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- PDB-3zmf: Salmonella enterica SadA 303-358 fused to GCN4 adaptors (SadAK2) -

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Basic information

Entry
Database: PDB / ID: 3zmf
TitleSalmonella enterica SadA 303-358 fused to GCN4 adaptors (SadAK2)
ComponentsGENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4
KeywordsMEMBRANE PROTEIN / DALL DOMAIN / DALL2 / TAA
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) / 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 ...Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / 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
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: 1.85 Å
AuthorsHartmann, M.D. / Hernandez Alvarez, B. / Albrecht, R. / Lupas, A.N.
Citation
Journal: Protein Eng.Des.Sel. / Year: 2008
Title: A New Expression System for Protein Crystallization Using Trimeric Coiled-Coil Adaptors.
Authors: Hernandez Alvarez, B. / Hartmann, M.D. / Albrecht, R. / Lupas, A.N. / Zeth, K. / Linke, D.
#1: Journal: 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
DepositionFeb 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Source and taxonomy
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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, GENERAL CONTROL PROTEIN GCN4
B: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4
C: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)37,4473
Polymers37,4473
Non-polymers00
Water2,216123
1
C: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4

C: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4

C: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)37,4473
Polymers37,4473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_355-x+y-2,-x,z1
crystal symmetry operation2_575-y,x-y+2,z1
Buried area13180 Å2
ΔGint-150.7 kcal/mol
Surface area16570 Å2
MethodPISA
2
B: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4

B: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4

B: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)37,4473
Polymers37,4473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area13400 Å2
ΔGint-145.7 kcal/mol
Surface area16460 Å2
MethodPISA
3
A: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4

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

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


Theoretical massNumber of molelcules
Total (without water)37,4473
Polymers37,4473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area13260 Å2
ΔGint-140 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.590, 46.590, 128.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-2002-

HOH

21A-2025-

HOH

31B-2015-

HOH

41B-2039-

HOH

51C-2009-

HOH

61C-2025-

HOH

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Components

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


Mass: 12482.168 Da / Num. of mol.: 3
Fragment: GCN4 ADAPTOR RESIDUES 250-278, ADHESIN RESIDUES 303-358, GCN4 ADAPTOR RESIDUES 250-278
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growDetails: 50% PEG 200, 0.1 M NA-CITRATE PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9686
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 31, 2007
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.726
11K, H, -L20.274
ReflectionResolution: 1.85→38.5 Å / Num. obs: 26591 / % possible obs: 99.2 % / Redundancy: 3.72 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.2
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 3.15 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.9 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCM

1gcm


Resolution: 1.85→38.51 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.911 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22051 1316 4.9 %RANDOM
Rwork0.18135 ---
obs0.18325 25273 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.523 Å2
Baniso -1Baniso -2Baniso -3
1-15.21 Å20 Å20 Å2
2--15.21 Å20 Å2
3----30.42 Å2
Refinement stepCycle: LAST / Resolution: 1.85→38.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 0 123 2545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0192448
X-RAY DIFFRACTIONr_bond_other_d0.0040.022355
X-RAY DIFFRACTIONr_angle_refined_deg2.1471.9553327
X-RAY DIFFRACTIONr_angle_other_deg1.06435398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9085332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.75427.24187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.23515424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.793152
X-RAY DIFFRACTIONr_chiral_restr0.1440.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022788
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02472
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 98 -
Rwork0.21 1789 -
obs--95.3 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3907-0.16-1.3033.117-4.488314.1742-0.09550.0213-0.17440.2359-0.2734-0.07210.1750.90010.36890.2038-0.0093-0.0780.3761-0.07090.25314.683-2.887-53.557
20.1050.1759-0.82860.3576-1.381815.2602-0.04930.0156-0.0152-0.059-0.0407-0.0538-0.41440.510.090.17240.0196-0.01610.24850.01350.1025-17.8612.719-33.692
30.1148-0.1974-0.7351.234-1.104913.8419-0.08220.0576-0.0665-0.0743-0.21770.11130.4799-0.1790.30.2136-0.02050.05860.2372-0.04490.0717-47.10921.63692.936
40.564-0.55122.11991.3263-0.527217.93730.03470.1669-0.1301-0.1097-0.09510.0448-0.2488-0.12620.06040.19980.0118-0.01070.1888-0.09430.1732-0.05-5.985-24.115
52.5302-1.3629-0.01711.0892-2.215613.9414-0.01420.1362-0.00480.0125-0.0522-0.0101-0.0228-0.1330.06630.0876-0.0091-0.00320.033-0.01320.1783-20.4318.102-3.414
62.1823-1.2741-4.36760.84853.402620.2399-0.1925-0.22860.07250.11970.0102-0.02420.07570.30540.18230.127-0.0486-0.03190.272-0.01330.1384-41.44923.8863.038
71.23820.04580.33180.4949-0.08370.64140.01430.0689-0.0307-0.04480.03610.0344-0.0017-0.0383-0.05050.03050.00750.00150.01370.00740.1866-1.497-0.567-2.377
80.5738-0.06380.29431.10650.1740.62920.0075-0.0059-0.02590.039-0.00610.02830.0038-0.0382-0.00140.00660.00430.00560.0151-0.00050.1634-24.14612.12718.264
90.42270.01570.07180.76530.35021.25340.02220.0060.05510.0129-0.0015-0.02390.01650.0107-0.02070.0320.0089-0.00090.03810.00340.1755-45.46928.03841.5
100.59960.1616-2.24340.3101-0.923110.4337-0.0584-0.0339-0.02820.0435-0.0380.00340.17050.05340.09630.07240.00230.01190.01290.0030.20862.767-4.99631.837
110.30520.0322-0.19410.7692-2.141511.8623-0.0497-0.0958-0.08310.0871-0.040.00830.01160.19880.08960.06290.01070.00010.09240.01470.191-18.22411.63752.441
120.58920.195-1.29680.7244-1.065710.551-0.02170.06510.0269-0.0332-0.05190.01190.0694-0.02190.07360.01860.01510.00420.02850.00770.1859-43.4722.0676.972
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A277 - 303
2X-RAY DIFFRACTION2B277 - 303
3X-RAY DIFFRACTION3C277 - 303
4X-RAY DIFFRACTION4A304 - 317
5X-RAY DIFFRACTION5B304 - 317
6X-RAY DIFFRACTION6C304 - 317
7X-RAY DIFFRACTION7A318 - 358
8X-RAY DIFFRACTION8B318 - 358
9X-RAY DIFFRACTION9C318 - 358
10X-RAY DIFFRACTION10A359 - 387
11X-RAY DIFFRACTION11B359 - 387
12X-RAY DIFFRACTION12C359 - 387

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