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- PDB-7o9v: hypothetical protein OMM_04225 residues 244-274 from Candidatus M... -

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Basic information

Entry
Database: PDB / ID: 7o9v
Titlehypothetical protein OMM_04225 residues 244-274 from Candidatus Magnetoglobus multicellularis fused to GCN4 adaptors
ComponentsGeneral control transcription factor GCN4,hypothetical protein OMM_04225 residues 244-274 from Candidatus Magnetoglobus multicellularis 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 / Oxidative Stress Induced Senescence / nitrogen catabolite activation of transcription from RNA polymerase II promoter / 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 / Oxidative Stress Induced Senescence / nitrogen catabolite activation of transcription from RNA polymerase II promoter / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / amino acid biosynthetic process / 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 / 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
FG-GAP-like repeat / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / FG-GAP repeat / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Integrin alpha, N-terminal / Fibronectin type 3 domain ...FG-GAP-like repeat / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / FG-GAP repeat / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Integrin alpha, N-terminal / Fibronectin type 3 domain / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Uncharacterized protein / General control transcription factor GCN4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Candidatus Magnetoglobus multicellularis str. Araruama (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsAdlakha, J. / Albrecht, R. / Hartmann, M.D.
CitationJournal: To Be Published
Title: hypothetical protein OMM_04225 residues 244-274 from Candidatus Magnetoglobus multicellularis fused to GCN4 adaptors
Authors: Adlakha, J.
History
DepositionApr 17, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General control transcription factor GCN4,hypothetical protein OMM_04225 residues 244-274 from Candidatus Magnetoglobus multicellularis fused to GCN4 adaptors,General control transcription factor GCN4
B: General control transcription factor GCN4,hypothetical protein OMM_04225 residues 244-274 from Candidatus Magnetoglobus multicellularis fused to GCN4 adaptors,General control transcription factor GCN4
C: General control transcription factor GCN4,hypothetical protein OMM_04225 residues 244-274 from Candidatus Magnetoglobus multicellularis fused to GCN4 adaptors,General control transcription factor GCN4


Theoretical massNumber of molelcules
Total (without water)32,4593
Polymers32,4593
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-111 kcal/mol
Surface area14460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.827, 34.649, 82.547
Angle α, β, γ (deg.)90.000, 93.480, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA216 - 2956 - 85
21GLUGLUBB216 - 2956 - 85
12ILEILEAA216 - 2966 - 86
22ILEILECC216 - 2966 - 86
13GLUGLUBB216 - 2956 - 85
23GLUGLUCC216 - 2956 - 85

NCS ensembles :
ID
1
2
3

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Components

#1: Protein General control transcription factor GCN4,hypothetical protein OMM_04225 residues 244-274 from Candidatus Magnetoglobus multicellularis fused to GCN4 adaptors,General control transcription factor GCN4 / Amino acid biosynthesis regulatory protein / General control protein GCN4


Mass: 10819.589 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Candidatus Magnetoglobus multicellularis str. Araruama (bacteria)
Strain: ATCC 204508 / S288c / Gene: GCN4, AAS101, AAS3, ARG9, YEL009C, OMM_04225 / Production host: Escherichia coli (E. coli) / References: UniProt: P03069, UniProt: A0A1V1P2N3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 1.88 Å3/Da / Density % sol: 34.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2M KSCN, 0.1M bis tris propane pH 8.5, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→37.04 Å / Num. obs: 11390 / % possible obs: 89.3 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Net I/σ(I): 8.5
Reflection shellResolution: 1.99→2.12 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.671 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 570 / CC1/2: 0.657 / % possible all: 81.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YNY

2yny


Resolution: 1.99→37.04 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.884 / SU B: 19.611 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.563 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3149 779 6.8 %RANDOM
Rwork0.2618 ---
obs0.2656 10611 67.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.27 Å2 / Biso mean: 44.231 Å2 / Biso min: 15.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å21.18 Å2
2--1.16 Å2-0 Å2
3----2.09 Å2
Refinement stepCycle: final / Resolution: 1.99→37.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 0 26 2052
Biso mean---35.05 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192051
X-RAY DIFFRACTIONr_bond_other_d0.0060.022026
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.9742755
X-RAY DIFFRACTIONr_angle_other_deg1.40134697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9645243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.64126.91594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55615441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.155153
X-RAY DIFFRACTIONr_chiral_restr0.0990.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022215
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02396
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A39190.16
12B39190.16
21A38910.16
22C38910.16
31B37900.17
32C37900.17
LS refinement shellResolution: 1.99→2.041 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 13 -
Rwork0.375 187 -
all-200 -
obs--15.63 %
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)
12.48081.1208-3.96192.574-2.92614.538-0.04530.0311-0.01830.03320.0081-0.0993-0.29810.0010.03720.03970.0268-0.03970.0518-0.01840.181720.915-1.4191.966
22.5942-1.4649-4.3941.81072.078814.9035-0.06970.0118-0.0882-0.0460.0104-0.01410.14850.14550.05930.0441-0.0298-0.05660.04740.00480.216912.371-3.119-1.308
31.71680.01241.41941.26130.642515.5186-0.03060.0189-0.0143-0.0025-0.00950.08030.0478-0.00860.040.0585-0.0093-0.00230.00340.01830.214615.065.8760.525
44.06760.2462-9.55640.6237-1.273623.96540.87210.44650.5661-0.02130.11180.0844-1.7349-1.3776-0.9840.40180.03050.13290.37010.00540.42195.5482.28940.558
54.47261.1899-7.56561.4029-5.579924.51520.41960.36560.2514-0.0753-0.2073-0.0058-0.11360.3907-0.21230.39460.06330.05230.33560.00130.17225.8350.46240.52
65.5281.7988-7.63580.7293-1.588117.13980.23950.51670.08260.05250.10230.0586-0.2804-1.2225-0.34190.39220.10530.12790.390.08280.32894.4020.90539.824
73.29420.8314-4.87811.93570.125213.4596-0.0128-0.0757-0.04440.08180.10530.04950.0040.1721-0.09250.0570.0428-0.06850.0640.00490.2088-2.977-2.40476.042
83.4304-0.7093-7.12411.58961.801917.257-0.06360.0510.0539-0.10510.00410.0336-0.1510.07850.05960.0505-0.0183-0.07150.12770.01330.2174-12.848-1.57573.475
91.91710.1316-2.01920.82280.43279.4450.07210.13810.0986-0.1278-0.0072-0.0858-0.1465-0.0247-0.06490.17370.0192-0.01580.0199-0.01120.2693-7.8076.03375.169
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A216 - 245
2X-RAY DIFFRACTION2B215 - 245
3X-RAY DIFFRACTION3C216 - 245
4X-RAY DIFFRACTION4A246 - 270
5X-RAY DIFFRACTION5B246 - 270
6X-RAY DIFFRACTION6C246 - 270
7X-RAY DIFFRACTION7A271 - 296
8X-RAY DIFFRACTION8B271 - 298
9X-RAY DIFFRACTION9C271 - 296

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