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- PDB-1c94: REVERSING THE SEQUENCE OF THE GCN4 LEUCINE ZIPPER DOES NOT AFFECT... -

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Basic information

Entry
Database: PDB / ID: 1c94
TitleREVERSING THE SEQUENCE OF THE GCN4 LEUCINE ZIPPER DOES NOT AFFECT ITS FOLD.
ComponentsRETRO-GCN4 LEUCINE ZIPPER
KeywordsGENE REGULATION / RETRO-COILED COIL / 4-ALPHA-HELIX-BUNDLE / PEPTIDE SYNTHESIS
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.08 Å
AuthorsMittl, P.R.E. / Deillon, C.A. / Sargent, D. / Liu, N. / Klauser, S. / Thomas, R.M. / Gutte, B. / Gruetter, M.G.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The retro-GCN4 leucine zipper sequence forms a stable three-dimensional structure.
Authors: Mittl, P.R. / Deillon, C. / Sargent, D. / Liu, N. / Klauser, S. / Thomas, R.M. / Gutte, B. / Grutter, M.G.
#1: Journal: Science / Year: 1991
Title: X-Ray Structure of the GCN4 Leucine Zipper, a Two-Stranded, Parallel Coiled Coil.
Authors: O'Shea, E.K. / Klemm, J.D. / Kim, P.S. / Alber, T.
#2: Journal: Science / Year: 1993
Title: A Switch Between Two-, Three-, and Four-Stranded Coiled Coils in GCN4 Leucine Zipper Mutants.
Authors: Harbury, P.B. / Zhang, T. / Kim, P.S. / Alber, T.
History
DepositionJul 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 14, 2019Group: Data collection / Category: computing
Revision 1.6Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RETRO-GCN4 LEUCINE ZIPPER
B: RETRO-GCN4 LEUCINE ZIPPER


Theoretical massNumber of molelcules
Total (without water)8,9282
Polymers8,9282
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-14 kcal/mol
Surface area6320 Å2
MethodPISA
2
A: RETRO-GCN4 LEUCINE ZIPPER
B: RETRO-GCN4 LEUCINE ZIPPER

A: RETRO-GCN4 LEUCINE ZIPPER
B: RETRO-GCN4 LEUCINE ZIPPER


Theoretical massNumber of molelcules
Total (without water)17,8574
Polymers17,8574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6720 Å2
ΔGint-58 kcal/mol
Surface area9090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.110, 34.090, 56.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein/peptide RETRO-GCN4 LEUCINE ZIPPER


Mass: 4464.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 1.84 Å3/Da / Density % sol: 33.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 25% 2-METHYL-2,4-PENTANEDIOL, 100 MM SODIUM ACETATE, 200 MM SODIUM CHLORIDE., pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Details: drop contained 1:1 mixture of peptide and reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mg/mlpeptide1drop
20.2 Msodium chloride1reservoir
325 %(v/v)MPD1reservoir
4100 mMsodium acetate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF BM1A10.873
2
Detector
TypeIDDetectorDate
MARRESEARCH1AREA DETECTORApr 28, 1999
2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.08→20 Å / Num. all: 4280 / Num. obs: 3740 / % possible obs: 87.4 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.035
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.11 / % possible all: 80.7
Reflection
*PLUS
% possible obs: 87.2 %
Reflection shell
*PLUS
% possible obs: 80.7 %

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Processing

Software
NameClassification
X-PLORrefinement
CNSrefinement
AMoREphasing
REFMACrefinement
MAR345data collection
XDSdata scaling
RefinementResolution: 2.08→20 Å / σ(F): 0 / σ(I): 0
Stereochemistry target values: CNS-TOPPAR PROTEIN_REP.PARAM CNS-TOPPAR WATER_REP.PARAM
Details: PHASE SOLUTION FOUND THROUGH MOLECULAR REPLACEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2805 293 -RANDOM
Rwork0.1803 ---
obs0.1803 3740 87.2 %-
all-4280 --
Refinement stepCycle: LAST / Resolution: 2.08→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms610 0 0 59 669
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0341
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.1023
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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