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- PDB-1kd9: X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACI... -

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Basic information

Entry
Database: PDB / ID: 1kd9
TitleX-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12La16L BASE-d12La16L
Components
  • GCN4 ACID BASE HETERODIMER ACID-d12La16L
  • GCN4 ACID BASE HETERODIMER BASE-d12La16L
KeywordsDE NOVO PROTEIN / coiled coil heterodimer
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKeating, A.E. / Malashkevich, V.N. / Tidor, B. / Kim, P.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils.
Authors: Keating, A.E. / Malashkevich, V.N. / Tidor, B. / Kim, P.S.
History
DepositionNov 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GCN4 ACID BASE HETERODIMER ACID-d12La16L
B: GCN4 ACID BASE HETERODIMER BASE-d12La16L
C: GCN4 ACID BASE HETERODIMER ACID-d12La16L
D: GCN4 ACID BASE HETERODIMER BASE-d12La16L
E: GCN4 ACID BASE HETERODIMER BASE-d12La16L
F: GCN4 ACID BASE HETERODIMER ACID-d12La16L


Theoretical massNumber of molelcules
Total (without water)24,9416
Polymers24,9416
Non-polymers00
Water3,135174
1
A: GCN4 ACID BASE HETERODIMER ACID-d12La16L
B: GCN4 ACID BASE HETERODIMER BASE-d12La16L


Theoretical massNumber of molelcules
Total (without water)8,3142
Polymers8,3142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-21 kcal/mol
Surface area5030 Å2
MethodPISA
2
C: GCN4 ACID BASE HETERODIMER ACID-d12La16L
D: GCN4 ACID BASE HETERODIMER BASE-d12La16L


Theoretical massNumber of molelcules
Total (without water)8,3142
Polymers8,3142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-25 kcal/mol
Surface area5180 Å2
MethodPISA
3
E: GCN4 ACID BASE HETERODIMER BASE-d12La16L
F: GCN4 ACID BASE HETERODIMER ACID-d12La16L


Theoretical massNumber of molelcules
Total (without water)8,3142
Polymers8,3142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-25 kcal/mol
Surface area5120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.740, 86.740, 79.176
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe assembly is a dimer. There are three copies of the dimer intact in the asymmetric unit.

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Components

#1: Protein/peptide GCN4 ACID BASE HETERODIMER ACID-d12La16L / GABH ALL


Mass: 4156.490 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#2: Protein/peptide GCN4 ACID BASE HETERODIMER BASE-d12La16L / GABH BLL


Mass: 4157.150 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.982 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: PEG 4000, Na Hepes, 2-propanol, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
218-20 %PEG40001reservoir
30.1 Msodium HEPES1reservoirpH7.7
410 %2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 19, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. all: 20141 / Num. obs: 20141 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.04
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.337 / % possible all: 99.4
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 35 Å / Rmerge(I) obs: 0.04

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: calculated structure

Resolution: 2.1→10 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2963 1788 10.1 %random
Rwork0.2417 ---
all-17771 --
obs-17771 98.8 %-
Solvent computationSolvent model: flat model / Bsol: 91.0823 Å2 / ksol: 0.440279 e/Å3
Displacement parametersBiso mean: 58.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2--1.01 Å20 Å2
3----2.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 0 174 1822
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013009
X-RAY DIFFRACTIONc_angle_deg1.40254
X-RAY DIFFRACTIONc_dihedral_angle_d14.8
X-RAY DIFFRACTIONc_improper_angle_d0.98
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 302 10.3 %
Rwork0.309 2624 -
obs--99.4 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 58.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg14.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / Rfactor Rfree: 0.374 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.309

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