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- PDB-1kdd: X-ray structure of the coiled coil GCN4 ACID BASE HETERODIMER ACI... -

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Basic information

Entry
Database: PDB / ID: 1kdd
TitleX-ray structure of the coiled coil GCN4 ACID BASE HETERODIMER ACID-d12La16I BASE-d12La16L
Components
  • GCN4 ACID BASE HETERODIMER ACID-d12La16I
  • GCN4 ACID BASE HETERODIMER BASE-d12La16L
KeywordsDE NOVO PROTEIN / coiled coil heterodimer
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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 1.4Nov 6, 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
B: GCN4 ACID BASE HETERODIMER BASE-d12La16L
A: GCN4 ACID BASE HETERODIMER ACID-d12La16I
D: GCN4 ACID BASE HETERODIMER BASE-d12La16L
C: GCN4 ACID BASE HETERODIMER ACID-d12La16I
E: GCN4 ACID BASE HETERODIMER BASE-d12La16L
F: GCN4 ACID BASE HETERODIMER ACID-d12La16I


Theoretical massNumber of molelcules
Total (without water)24,9416
Polymers24,9416
Non-polymers00
Water2,036113
1
B: GCN4 ACID BASE HETERODIMER BASE-d12La16L
A: GCN4 ACID BASE HETERODIMER ACID-d12La16I


Theoretical massNumber of molelcules
Total (without water)8,3142
Polymers8,3142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-22 kcal/mol
Surface area5100 Å2
MethodPISA
2
D: GCN4 ACID BASE HETERODIMER BASE-d12La16L
C: GCN4 ACID BASE HETERODIMER ACID-d12La16I


Theoretical massNumber of molelcules
Total (without water)8,3142
Polymers8,3142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-20 kcal/mol
Surface area4770 Å2
MethodPISA
3
E: GCN4 ACID BASE HETERODIMER BASE-d12La16L
F: GCN4 ACID BASE HETERODIMER ACID-d12La16I


Theoretical massNumber of molelcules
Total (without water)8,3142
Polymers8,3142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-22 kcal/mol
Surface area5110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.278, 86.278, 78.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-56-

HOH

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 BASE-d12La16L / GABH BLL


Mass: 4157.150 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#2: Protein/peptide GCN4 ACID BASE HETERODIMER ACID-d12La16I / GABH ALI


Mass: 4156.490 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.: 113 / 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: 2.939 Å3/Da / Density % sol: 56.5 %
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: 1.0093 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 19, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 2.05→35 Å / Num. all: 18925 / Num. obs: 18925 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.257 / % possible all: 96.3
Reflection
*PLUS
Lowest resolution: 35 Å / Rmerge(I) obs: 0.06

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Processing

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

Resolution: 2.14→19.91 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
Rfree0.3022 1682 10.1 %random
Rwork0.2523 ---
all-16580 --
obs-16580 97.8 %-
Solvent computationSolvent model: flat model / Bsol: 52.247 Å2 / ksol: 0.341169 e/Å3
Displacement parametersBiso mean: 59.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.94 Å20 Å20 Å2
2--2.94 Å20 Å2
3----5.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.14→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 0 113 1706
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004438
X-RAY DIFFRACTIONc_angle_deg0.8315
X-RAY DIFFRACTIONc_dihedral_angle_d13.1
X-RAY DIFFRACTIONc_improper_angle_d0.62
LS refinement shellResolution: 2.14→2.27 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 267 9.9 %
Rwork0.309 2437 -
obs--97.9 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor obs: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 59.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg13.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.62
LS refinement shell
*PLUS
Rfactor Rfree: 0.354 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.309

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