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- PDB-5app: Actinobacillus actinomycetemcomitans OMP100 residues 133-198 fuse... -

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Basic information

Entry
Database: PDB / ID: 5app
TitleActinobacillus actinomycetemcomitans OMP100 residues 133-198 fused to GCN4 adaptors
ComponentsGeneral control protein GCN4,GENERAL CONTROL PROTEIN GCN4, OUTER MEMBRANE PROTEIN 100,General control protein GCN4
KeywordsMEMBRANE PROTEIN / FUSION PROTEIN / ALPHA/BETA COILED COIL / BETA LAYER / TRIMER / 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 / RNA polymerase II transcription regulator complex / : / 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 / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
AGGREGATIBACTER ACTINOMYCETEMCOMITANS D11S-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHartmann, M.D. / Ridderbusch, O. / Lupas, A.N. / Hernandez Alvarez, B.
CitationJournal: Elife / Year: 2016
Title: alpha / beta coiled coils.
Authors: Hartmann, M.D. / Mendler, C.T. / Bassler, J. / Karamichali, I. / Ridderbusch, O. / Lupas, A.N. / Hernandez Alvarez, B.
History
DepositionSep 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references / Source and taxonomy
Revision 1.2Sep 25, 2019Group: Data collection / Database references ...Data collection / Database references / Other / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_database_status / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity.pdbx_mutation / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.3Jan 10, 2024Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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,GENERAL CONTROL PROTEIN GCN4, OUTER MEMBRANE PROTEIN 100,General control protein GCN4
B: General control protein GCN4,GENERAL CONTROL PROTEIN GCN4, OUTER MEMBRANE PROTEIN 100,General control protein GCN4
C: General control protein GCN4,GENERAL CONTROL PROTEIN GCN4, OUTER MEMBRANE PROTEIN 100,General control protein GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5028
Polymers46,3253
Non-polymers1775
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14100 Å2
ΔGint-137.9 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.130, 35.860, 198.510
Angle α, β, γ (deg.)90.00, 96.02, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 182
2115B1 - 182
3115C1 - 182
1125A191 - 231
2125B191 - 231
3125C191 - 231

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.493852, 0.869529, -0.005477), (-0.8695, -0.493881, -0.007121), (-0.008897, 0.001246, 0.99996)-15.94932, -9.46532, -0.13238
3given(-0.533148, -0.845993, -0.007004), (0.846017, -0.533097, -0.007904), (0.002953, -0.010139, 0.999944)-16.46849, 8.4553, -0.04291

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Components

#1: Protein General control protein GCN4,GENERAL CONTROL PROTEIN GCN4, OUTER MEMBRANE PROTEIN 100,General control protein GCN4 / Amino acid biosynthesis regulatory protein


Mass: 15441.728 Da / Num. of mol.: 3
Fragment: UNP RESIDUES P03069 250-277, G4B386 133-199, P03069 250-277,UNP RESIDUES P03069 250-277, G4B386 133-199, P03069 250-277,UNP RESIDUES P03069 250-277, G4B386 133-199, P03069 250-277
Mutation: YES,YES,YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) AGGREGATIBACTER ACTINOMYCETEMCOMITANS D11S-1 (bacteria)
Strain: ATCC 204508 / S288c / Gene: GCN4, AAS3, ARG9, YEL009C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03069
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growDetails: 0.1 M TRI-SODIUM CITRATE PH 5.5, 2 %(V/V) DIOXANE 15 %(W/V) PEG 10,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.315
111/2H-3/2K, -1/2H-1/2K, -1/2H+1/2K-L20.343
111/2H+3/2K, 1/2H-1/2K, -1/2H-1/2K-L30.342
ReflectionResolution: 2.3→32.9 Å / Num. obs: 18247 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Redundancy: 2.84 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 2.52 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.88 / % possible all: 86.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WPQ

2wpq


Resolution: 2.3→32.9 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.99 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25407 956 5.2 %RANDOM
Rwork0.22478 ---
obs0.22628 17278 92.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.347 Å2
Baniso -1Baniso -2Baniso -3
1-27.89 Å20 Å2-1.57 Å2
2--18.44 Å20 Å2
3----46.33 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 5 35 2975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192947
X-RAY DIFFRACTIONr_bond_other_d0.0010.022974
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.9613958
X-RAY DIFFRACTIONr_angle_other_deg0.74336820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5735380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.0326.172128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.99715601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1991517
X-RAY DIFFRACTIONr_chiral_restr0.0570.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02584
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_it1.7614.6441529
X-RAY DIFFRACTIONr_mcbond_other1.7564.6441528
X-RAY DIFFRACTIONr_mcangle_it2.6496.961906
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8124.7951418
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A467medium positional0.250.5
12B467medium positional0.250.5
13C467medium positional0.260.5
21A246medium positional0.250.5
22B246medium positional0.250.5
23C246medium positional0.240.5
11A662loose positional0.575
12B662loose positional0.525
13C662loose positional0.515
21A393loose positional0.515
22B393loose positional0.65
23C393loose positional0.575
11A467medium thermal1.882
12B467medium thermal1.992
13C467medium thermal2.462
21A246medium thermal1.792
22B246medium thermal2.342
23C246medium thermal1.942
11A662loose thermal2.9910
12B662loose thermal2.7310
13C662loose thermal3.1310
21A393loose thermal2.1310
22B393loose thermal3.1110
23C393loose thermal2.9410
LS refinement shellResolution: 2.303→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 83 -
Rwork0.239 1101 -
obs--82.62 %
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)
10.32790.02330.40190.1119-0.27797.7307-0.0079-0.0439-0.02930.03920.00210.00240.0622-0.02630.00580.01990.00430.00810.00660.01050.1641-12.3177-0.0902-59.5933
25.4051-0.95364.19648.0634-4.28774.8571-0.2006-0.06310.1117-0.42670.20020.31710.0306-0.12040.00040.3543-0.0073-0.06220.2642-0.05640.4609-11.6173-5.46997.2279
30.7732-0.1124-0.76351.13092.75878.7179-0.04670.0726-0.006-0.0097-0.13460.04050.199-0.18920.18130.04690.00710.00910.04440.00840.165-14.67242.113345.2346
40.2923-0.0848-0.3230.23510.66618.2359-0.0173-0.0312-0.03380.0476-0.038-0.0297-0.0183-0.1270.05530.0136-0.0069-0.00270.01390.01090.1613-9.674-1.5293-60.2487
511.2969-0.3022-6.48351.62460.6073.83950.3093-0.28340.00040.1237-0.44860.4297-0.14020.05470.13930.18720.00030.00060.2846-0.01690.3357-4.78591.25277.2883
60.94930.1656-1.79440.4851-0.73168.4149-0.0650.0448-0.0268-0.0496-0.0956-0.0149-0.04170.16860.16070.0406-0.00720.00990.0608-0.01110.1579-10.2965-4.902846.1446
70.26530.0789-0.55540.2424-0.45797.3638-0.0292-0.0751-0.00510.0369-0.0435-0.012-0.1036-0.05340.07280.01510.00730.00770.034-0.01180.1571-9.77121.7254-60.4682
81.3197-0.1737-0.24190.03010.0230.0555-0.04040.1755-0.00350.0087-0.0166-0.04250.0077-0.03250.0570.13510.0024-0.01420.14220.00160.2608-14.16384.18627.3588
90.9446-0.10282.08481.1902-1.48938.3935-0.1960.0890.04670.0069-0.1402-0.0017-0.32050.07890.33620.0575-0.00850.01880.0758-0.00230.1672-6.05022.876945.6843
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 182
2X-RAY DIFFRACTION2A183 - 190
3X-RAY DIFFRACTION3A191 - 231
4X-RAY DIFFRACTION4B1 - 182
5X-RAY DIFFRACTION5B183 - 190
6X-RAY DIFFRACTION6B191 - 231
7X-RAY DIFFRACTION7C1 - 182
8X-RAY DIFFRACTION8C183 - 190
9X-RAY DIFFRACTION9C191 - 231

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