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- PDB-3w92: Crystal Structure Analysis of the synthetic GCN4 Thioester coiled... -

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Basic information

Entry
Database: PDB / ID: 3w92
TitleCrystal Structure Analysis of the synthetic GCN4 Thioester coiled coil peptide
ComponentsThioester coiled coil peptide
KeywordsTRANSCRIPTION
Function / homologyACETATE ION / PARA ACETAMIDO BENZOIC ACID
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 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 24, 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,94812
Polymers10,8103
Non-polymers1,1389
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-18 kcal/mol
Surface area7750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.760, 33.552, 94.998
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 Thioester coiled coil peptide


Mass: 3603.410 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: This sequence occurs naturally in GCN4 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.34 Å3/Da / Density % sol: 47.46 % / Mosaicity: 0.56 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.2M Sodium Acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 23001 / Num. obs: 22947 / % possible obs: 99.8 % / Redundancy: 24.8 % / Rmerge(I) obs: 0.082 / Χ2: 2.3 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.35-1.3720.10.87611031.437199
1.37-1.4210.84411571.461199.9
1.4-1.4323.10.86910881.4971100
1.43-1.4523.80.67511391.62199.9
1.45-1.4925.30.49711311.6371100
1.49-1.5225.40.35811291.7411100
1.52-1.5626.30.37511101.7311100
1.56-1.626.40.35811541.8011100
1.6-1.6526.50.29611331.8231100
1.65-1.726.40.25111291.8651100
1.7-1.7626.40.21611501.9551100
1.76-1.8326.60.18411192.0651100
1.83-1.9226.30.15711502.2631100
1.92-2.0226.10.12411452.5911100
2.02-2.1425.60.10911483.1591100
2.14-2.3124.80.08911713.6161100
2.31-2.5424.80.08211493.6241100
2.54-2.9124.50.06511883.4681100
2.91-3.6624.30.04711943.221199.8
3.66-5022.10.04212603.021197.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IJ2, 1IJ3

1ij2

1ij3


Resolution: 1.35→47.5 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8508 / SU B: 2.065 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1895 1174 5.1 %RANDOM
Rwork0.1639 ---
obs0.1653 22857 99.47 %-
all-23001 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.33 Å2 / Biso mean: 21.2541 Å2 / Biso min: 10.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.82 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.35→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms753 0 76 115 944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.022884
X-RAY DIFFRACTIONr_bond_other_d0.0030.02706
X-RAY DIFFRACTIONr_angle_refined_deg2.5822.1561154
X-RAY DIFFRACTIONr_angle_other_deg1.24431714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9795102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.34222.59327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52815207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4941510
X-RAY DIFFRACTIONr_chiral_restr0.1290.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02914
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02191
X-RAY DIFFRACTIONr_mcbond_it2.1781.5494
X-RAY DIFFRACTIONr_mcbond_other1.651.5208
X-RAY DIFFRACTIONr_mcangle_it3.2672781
X-RAY DIFFRACTIONr_scbond_it4.3743390
X-RAY DIFFRACTIONr_scangle_it6.6354.5364
X-RAY DIFFRACTIONr_rigid_bond_restr2.20231590
X-RAY DIFFRACTIONr_sphericity_free17.2473115
X-RAY DIFFRACTIONr_sphericity_bonded11.68631594
LS refinement shellResolution: 1.352→1.387 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 73 -
Rwork0.227 1527 -
all-1600 -
obs--96.74 %
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)
10.0910.02880.11930.04280.0640.4199-0.00840.0117-0.0048-0.00180.0130.002-0.00550.028-0.00460.0309-0.00250.00160.0592-0.00140.0167-3.71912.8916-14.3634
20.02810.01880.06480.08230.14390.29640.00290.0022-0.0063-0.00380.00170.002-0.0072-0.0033-0.00470.0336-0.001-0.00060.05860.00050.0112-13.07773.6742-13.9268
30.0154-0.0199-0.12230.03360.18811.0943-0.0015-0.0028-0.0020.01270.0048-0.00070.05630.0087-0.00330.03520.0002-0.00020.0579-0.00010.0172-9.0157-4.1332-14.1241
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 32
2X-RAY DIFFRACTION1A101 - 105
3X-RAY DIFFRACTION1A201 - 241
4X-RAY DIFFRACTION2B1 - 32
5X-RAY DIFFRACTION2B101 - 102
6X-RAY DIFFRACTION2B201 - 237
7X-RAY DIFFRACTION3C1 - 32
8X-RAY DIFFRACTION3C101 - 102
9X-RAY DIFFRACTION3C201 - 237

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