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- PDB-3w8v: Crystal Structure Analysis of the synthetic GCN4 coiled coil peptide -

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Basic information

Entry
Database: PDB / ID: 3w8v
TitleCrystal Structure Analysis of the synthetic GCN4 coiled coil peptide
ComponentsGCN4n coiled coil peptide
KeywordsTRANSCRIPTION
Function / homologyPARA ACETAMIDO BENZOIC ACID
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsShahar, A. / Zarivach, R. / Ashkenasy, G.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: A high-resolution structure that provides insight into coiled-coil thiodepsipeptide dynamic chemistry
Authors: Dadon, Z. / Samiappan, M. / Shahar, A. / Zarivach, R. / Ashkenasy, G.
History
DepositionMar 21, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 8, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GCN4n coiled coil peptide
B: GCN4n coiled coil peptide
C: GCN4n coiled coil peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,77910
Polymers10,7593
Non-polymers1,0207
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-18 kcal/mol
Surface area7800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.168, 34.162, 95.067
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide GCN4n coiled coil peptide


Mass: 3586.360 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: This sequence occurs naturally in GCN4 proteins family
#2: Chemical
ChemComp-TYZ / PARA ACETAMIDO BENZOIC ACID


Mass: 179.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H9NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.35 Å3/Da / Density % sol: 47.7 % / Mosaicity: 0.927 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50% Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 8, 2011
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→23 Å / Num. all: 6348 / Num. obs: 6278 / % possible obs: 99.1 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.106 / Χ2: 2.113 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.146.90.4162821.765190.7
2.14-2.187.50.3662841.977195.3
2.18-2.228.40.3983121.864198.1
2.22-2.2690.2732922.123199.3
2.26-2.319.50.3483081.8641100
2.31-2.3610.40.3253171.798199.7
2.36-2.4210.20.3023131.738199.4
2.42-2.4910.70.2812891.911100
2.49-2.5611.20.2553231.8751100
2.56-2.65110.2253151.7791100
2.65-2.7411.40.2043061.9331100
2.74-2.8511.20.1623231.8851100
2.85-2.9811.30.1342962.2651100
2.98-3.1411.30.1313302.1561100
3.14-3.3311.30.1083102.3281100
3.33-3.5911.10.0823222.6391100
3.59-3.9511.10.0793252.7781100
3.95-4.5110.70.0633282.6111100
4.51-5.6710.70.0643352.2481100
5.67-239.30.0513682.306198.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å22.38 Å
Translation2.5 Å22.38 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.2.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IJ2

1ij2


Resolution: 2.1→22.38 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.2538 / WRfactor Rwork: 0.1738 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7971 / SU B: 13.837 / SU ML: 0.162 / SU R Cruickshank DPI: 0.2787 / SU Rfree: 0.2517 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.279 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.288 607 9.8 %RANDOM
Rwork0.192 ---
obs0.2007 6211 98.31 %-
all-6348 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 37.41 Å2 / Biso mean: 31.578 Å2 / Biso min: 2.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2--2.64 Å20 Å2
3----2.3 Å2
Refinement stepCycle: LAST / Resolution: 2.1→22.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms753 0 68 71 892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022814
X-RAY DIFFRACTIONr_angle_refined_deg2.0932.1911060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.035586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.85124.28621
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.86615172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.161156
X-RAY DIFFRACTIONr_chiral_restr0.0940.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02538
X-RAY DIFFRACTIONr_mcbond_it0.8811.5447
X-RAY DIFFRACTIONr_mcangle_it1.5072704
X-RAY DIFFRACTIONr_scbond_it2.8383367
X-RAY DIFFRACTIONr_scangle_it4.1294.5356
LS refinement shellResolution: 2.103→2.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 33 -
Rwork0.207 369 -
all-402 -
obs--89.73 %
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)
10.80450.39291.41560.42592.58215.2067-0.1037-0.05610.0773-0.1214-0.05980.0511-0.7272-0.24630.16350.16270.0297-0.01870.01950.00710.1526-8.82553.382814.318
20.4791-1.0195-0.12262.6852.43486.1436-0.1001-0.06490.02680.20870.13930.07730.41260.3596-0.03920.05980.0213-0.04490.1187-0.02350.1447-4.1934-3.6714.2375
30.55220.73751.28261.14721.07552.92870.0452-0.17280.03220.0923-0.25370.13880.1283-0.46020.20860.0172-0.0199-0.00510.1837-0.03260.1534-12.5201-4.847212.6315
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 32
2X-RAY DIFFRACTION1A101 - 102
3X-RAY DIFFRACTION1A201 - 220
4X-RAY DIFFRACTION2B1 - 32
5X-RAY DIFFRACTION2B101 - 102
6X-RAY DIFFRACTION2B201 - 227
7X-RAY DIFFRACTION3C1 - 32
8X-RAY DIFFRACTION3C101 - 103
9X-RAY DIFFRACTION3C201 - 224

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