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- PDB-5apz: Thermosinus carboxydivorans Nor1 Tcar0761 residues 68-101 and 191... -

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Basic information

Entry
Database: PDB / ID: 5apz
TitleThermosinus carboxydivorans Nor1 Tcar0761 residues 68-101 and 191-211 fused to GCN4 adaptors
ComponentsGENERAL CONTROL PROTEIN GCN4, NOR1 TCAR0761, GENERAL CONTROL PROTEIN GCN4
KeywordsDNA BINDING PROTEIN / ALPHA/BETA COILED COIL / BETA LAYER / TRIMER
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
Uncharacterized protein / General control transcription factor GCN4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
THERMOSINUS CARBOXYDIVORANS NOR1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHartmann, M.D. / Deiss, S. / 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 1.2Jan 10, 2024Group: 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, NOR1 TCAR0761, GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)13,9251
Polymers13,9251
Non-polymers00
Water1,874104
1
A: GENERAL CONTROL PROTEIN GCN4, NOR1 TCAR0761, GENERAL CONTROL PROTEIN GCN4

A: GENERAL CONTROL PROTEIN GCN4, NOR1 TCAR0761, GENERAL CONTROL PROTEIN GCN4

A: GENERAL CONTROL PROTEIN GCN4, NOR1 TCAR0761, GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)41,7763
Polymers41,7763
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area15510 Å2
ΔGint-146.7 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.920, 37.920, 179.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein GENERAL CONTROL PROTEIN GCN4, NOR1 TCAR0761, GENERAL CONTROL PROTEIN GCN4


Mass: 13925.276 Da / Num. of mol.: 1 / Fragment: RESIDUES 250-279,68-101,191-211,250-279
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast), (gene. exp.) THERMOSINUS CARBOXYDIVORANS NOR1 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03069, UniProt: A1HT30
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.8 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growDetails: 0.1 M TRI-SODIUM CITRATE PH 4.0, 30 %(V/V) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Aug 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→32.3 Å / Num. obs: 19111 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.69 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 20.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.65 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.23 / % possible all: 96.9

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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: 1.6→30.83 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.204 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21312 993 5.2 %RANDOM
Rwork0.17694 ---
obs0.17872 18113 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.659 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20.53 Å20 Å2
2--1.05 Å20 Å2
3----3.42 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms888 0 0 104 992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.019916
X-RAY DIFFRACTIONr_bond_other_d0.0010.02950
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.9961232
X-RAY DIFFRACTIONr_angle_other_deg0.87932202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7375118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.3927.17939
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98715207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.829153
X-RAY DIFFRACTIONr_chiral_restr0.1070.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021002
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02169
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_it2.2742.674455
X-RAY DIFFRACTIONr_mcbond_other2.2652.671454
X-RAY DIFFRACTIONr_mcangle_it2.884.002569
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.6693.375461
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: 1.598→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 68 -
Rwork0.317 1293 -
obs--94.51 %
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)
16.6090.0026-1.35844.5232-1.3131.22460.1131-0.18540.13570.2739-0.06170.0431-0.16760.0152-0.05140.1325-0.01530.01310.1259-0.02060.0922-6.327624.1842127.7372
20.37580.5154-0.1821.9441-0.717212.1282-0.019-0.0110.12140.1562-0.02080.2037-0.1316-0.03040.03980.0672-0.0132-0.00830.0942-0.00850.063-5.739620.5594119.41
30.464-0.4041-1.32460.8085-0.193810.02870.0114-0.03090.0333-0.0101-0.0102-0.0270.06250.0442-0.00120.0193-0.0155-0.00520.03540.00770.0388-3.333616.4057101.2718
40.7041-0.1425-0.22570.59151.0797.2909-0.0302-0.11-0.0780.0845-0.0809-0.06490.3036-0.28360.1110.0326-0.01820.00060.04070.02070.03080.593121.41359.1197
50.18390.2892-1.43890.6665-2.080411.74910.00180.00360.0150.0184-0.00550.04-0.0259-0.08120.00370.01770.00950.00070.0248-0.00570.04383.707317.79795.9464
62.71520.3919-1.27834.56361.840610.0161-0.01350.09380.0143-0.06580.0299-0.1442-0.0280.1415-0.01640.0013-0.00320.00020.02510.01480.01565.253424.4924-22.7728
78.7923-4.744810.397.2477-5.738612.63470.13560.57410.3649-0.8-0.49240.13390.22210.48640.35670.15420.0373-0.03090.16820.05950.06262.478826.8956-31.8061
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 7
2X-RAY DIFFRACTION2A8 - 14
3X-RAY DIFFRACTION3A15 - 32
4X-RAY DIFFRACTION4A33 - 69
5X-RAY DIFFRACTION5A70 - 100
6X-RAY DIFFRACTION6A101 - 108
7X-RAY DIFFRACTION7A109 - 999

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