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- PDB-7oaa: conserved hypothetical protein residues 311-335 from Candidatus M... -

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Entry
Database: PDB / ID: 7oaa
Titleconserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors
ComponentsGeneral control transcription factor GCN4,conserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors,General control transcription factor GCN4
KeywordsPROTEIN FIBRIL / Coiled Coil / beta layer / hexad repeat
Function / homology
Function and homology information


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 / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...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 / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / 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 / regulation of cell cycle / 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
Secreted protein / General control transcription factor GCN4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Candidatus Magnetomorum sp. HK-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAdlakha, J. / Albrecht, R. / Hartmann, M.D.
CitationJournal: To Be Published
Title: conserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors
Authors: Adlakha, J.
History
DepositionApr 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: General control transcription factor GCN4,conserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors,General control transcription factor GCN4


Theoretical massNumber of molelcules
Total (without water)10,1361
Polymers10,1361
Non-polymers00
Water1,63991
1
A: General control transcription factor GCN4,conserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors,General control transcription factor GCN4

A: General control transcription factor GCN4,conserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors,General control transcription factor GCN4

A: General control transcription factor GCN4,conserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors,General control transcription factor GCN4


Theoretical massNumber of molelcules
Total (without water)30,4083
Polymers30,4083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10590 Å2
ΔGint-97 kcal/mol
Surface area15350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.243, 38.243, 279.665
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-488-

HOH

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Components

#1: Protein General control transcription factor GCN4,conserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors,General control transcription factor GCN4 / Amino acid biosynthesis regulatory protein / General control protein GCN4


Mass: 10135.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Candidatus Magnetomorum sp. HK-1 (bacteria)
Strain: ATCC 204508 / S288c / Gene: GCN4, AAS101, AAS3, ARG9, YEL009C, MHK_004959 / Production host: Escherichia coli (E. coli) / References: UniProt: P03069, UniProt: A0A0N0D484
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1.94 Å3/Da / Density % sol: 36.65 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.5, 30% (w/v) PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0704 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0704 Å / Relative weight: 1
ReflectionResolution: 1.4→32.89 Å / Num. obs: 10751 / % possible obs: 91.5 % / Redundancy: 17.6 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Net I/σ(I): 24.3
Reflection shellResolution: 1.4→1.47 Å / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 538 / CC1/2: 0.978

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Processing

Software
NameVersionClassification
REFMAC5.8.0049 2013/06/30refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5apt

5apt


Resolution: 1.4→32.89 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.907 / SU ML: 0.071 / Cross valid method: FREE R-VALUE / ESU R: 0.128 / ESU R Free: 0.123
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2685 535 -
Rwork0.2308 10216 -
all0.233 --
obs-10751 65.981 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 18.816 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.145 Å20 Å2
2--0.29 Å20 Å2
3----0.939 Å2
Refinement stepCycle: LAST / Resolution: 1.4→32.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms692 0 0 91 783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.019722
X-RAY DIFFRACTIONr_bond_other_d0.0010.02761
X-RAY DIFFRACTIONr_angle_refined_deg0.6871.985965
X-RAY DIFFRACTIONr_angle_other_deg0.59631768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.029586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.53626.56332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66715175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.089152
X-RAY DIFFRACTIONr_chiral_restr0.0370.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02770
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02140
X-RAY DIFFRACTIONr_nbd_refined0.2020.2211
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1340.2647
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2331
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.2357
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.217
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1410.243
X-RAY DIFFRACTIONr_nbd_other0.1010.2128
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0520.211
X-RAY DIFFRACTIONr_mcbond_it1.3683.924336
X-RAY DIFFRACTIONr_mcbond_other1.2483.869335
X-RAY DIFFRACTIONr_mcangle_it2.2186.509420
X-RAY DIFFRACTIONr_mcangle_other2.2756.564421
X-RAY DIFFRACTIONr_scbond_it2.3085.314386
X-RAY DIFFRACTIONr_scbond_other2.2665.29386
X-RAY DIFFRACTIONr_scangle_it3.8348.378543
X-RAY DIFFRACTIONr_scangle_other3.8218.349543
X-RAY DIFFRACTIONr_lrange_it6.12320.039881
X-RAY DIFFRACTIONr_lrange_other6.0519.151856
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.4-1.4370.511120.319270118323.83770.292
1.437-1.4760.38470.303295116126.01210.254
1.476-1.5190.279160.259304110129.06450.225
1.519-1.5650.324240.28339107833.67350.232
1.565-1.6170.242140.256377106636.67920.224
1.617-1.6740.262250.251401101142.13650.204
1.674-1.7370.304270.279493101051.48510.234
1.737-1.8080.215300.26157495563.24610.223
1.808-1.8880.32390.26968489880.51230.239
1.888-1.980.309430.268328751000.219
1.98-2.0870.269430.25479984399.88140.24
2.087-2.2140.18390.2247567951000.199
2.214-2.3660.283380.2127227601000.191
2.366-2.5560.274360.2246757111000.206
2.556-2.80.285320.2116056371000.203
2.8-3.130.237300.21357460599.83470.213
3.13-3.6130.263270.2165075341000.231
3.613-4.4240.265220.18543545899.78170.203
4.424-6.2490.324190.24135037299.19360.273
6.249-93.2220.219120.26622423799.57810.321
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)
15.02091.68242.31784.87560.64159.3506-0.08880.2914-0.0397-0.39980.0113-0.07790.1338-0.1120.07750.05280.0087-0.01710.041-0.00130.1008-3.92545.030521.3295
21.0529-0.19630.7272.3173-0.39935.1701-0.06010.00330.0592-0.0116-0.04440.04-0.0513-0.10710.10450.04990.0032-0.00010.0377-0.00180.0609-1.81135.669736.0853
30.78980.31960.58811.9131-0.41686.7336-0.01170.05910.04970.0135-0.01850.0858-0.0877-0.08680.03030.05530.00370.00220.0434-0.00210.07081.48075.948651.1177
40.9238-1.48681.48543.2661-2.13136.79580.04050.1020.0052-0.1959-0.1633-0.08820.04370.37490.12280.02120.00510.01290.02150.00660.02233.5934-0.435766.462
53.00670.0018-1.06871.52512.59224.85280.00110.1846-0.0876-0.0311-0.16590.09630.017-0.37830.16490.0732-0.0209-0.03840.0384-0.0040.0271-4.6603-2.486480.6459
61.0268-0.2154-0.55041.34290.13766.0144-0.0134-0.134-0.05610.0314-0.03420.107-0.0234-0.08010.04760.0277-0.00410.00140.0306-0.00310.0599-7.11461.144795.5941
71.12290.3326-0.00731.21881.34839.9798-0.005-0.02290.04390.08720.04270.00270.08470.1489-0.03770.01370.01210.00980.02440.01140.0752-4.33153.9856118.8017
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
11282 - 291282 - 291
22292 - 301292 - 301
33302 - 311302 - 311
44312 - 321312 - 321
55322 - 331322 - 331
66332 - 341332 - 341
77342 - 363342 - 366

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