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- PDB-1uo5: Structure Based Engineering of Internal Molecular Surfaces Of Fou... -

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Basic information

Entry
Database: PDB / ID: 1uo5
TitleStructure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsFOUR HELIX BUNDLE / CAVITY / IODOBENZENE
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
iodobenzene / General control transcription factor GCN4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsYadav, M.K. / Redman, J.E. / Alvarez-Gutierrez, J.M. / Zhang, Y.
CitationJournal: Biochemistry / Year: 2005
Title: Structure-Based Engineering of Internal Cavities in Coiled-Coil Peptides
Authors: Yadav, M.K. / Redman, J.E. / Leman, L.J. / Alvarez-Gutierrez, J.M. / Zhang, Y. / Stout, C.D. / Ghadiri, M.R.
History
DepositionSep 15, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Jan 13, 2021Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GENERAL CONTROL PROTEIN GCN4
B: GENERAL CONTROL PROTEIN GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3014
Polymers8,0622
Non-polymers2392
Water18010
1
A: GENERAL CONTROL PROTEIN GCN4
B: GENERAL CONTROL PROTEIN GCN4
hetero molecules

A: GENERAL CONTROL PROTEIN GCN4
B: GENERAL CONTROL PROTEIN GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6028
Polymers16,1234
Non-polymers4794
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation24_555-z+3/4,-y+3/4,-x+3/41
MethodPQS
Unit cell
Length a, b, c (Å)78.490, 78.490, 78.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein/peptide GENERAL CONTROL PROTEIN GCN4 / GCN4 LEUCINE ZIPPER / AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN / PLI


Mass: 4030.757 Da / Num. of mol.: 2 / Mutation: YES / Source method: obtained synthetically
Details: BASED ON SEQUENCE FROM SACCHAROMYCES CEREVISIAE (BAKER'S YEAST)
Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P03069
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PIH / iodobenzene / Iodobenzene


Mass: 204.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE VAL 257 ALA, CHAINS A AND B

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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 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROP, RESERVOIR: 10%W/V PEG 6K, 2 M NACL, PH 7.0

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Data collection

DiffractionMean temperature: 114 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorDate: Feb 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.07→35.1 Å / Num. obs: 5435 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 14.6
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 6.83 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMACrefinement
CrystalClear(MSC/RIGAKU)data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→55.9 Å / SU B: 5.28 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.191
RfactorNum. reflection% reflectionSelection details
Rfree0.28305 245 4.5 %RANDOM
Rwork0.26137 ---
obs0.26238 5176 99.83 %-
Displacement parametersBiso mean: 46.672 Å2
Refinement stepCycle: LAST / Resolution: 2.07→55.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms514 0 8 10 532

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