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- PDB-4hjd: GCN4pLI derivative with alpha/beta/acyclic-gamma amino acid subst... -

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Basic information

Entry
Database: PDB / ID: 4hjd
TitleGCN4pLI derivative with alpha/beta/acyclic-gamma amino acid substitution pattern
ComponentsGCN4pLI(alpha/beta/acyclic gamma)
KeywordsUNKNOWN FUNCTION / alpha/beta/gamma amino acid
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsShin, Y.H. / Mortenson, D.E. / Satyshur, K.A. / Forest, K.T. / Gellman, S.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Differential Impact of beta and gamma Residue Preorganization on alpha / beta / gamma-Peptide Helix Stability in Water.
Authors: Shin, Y.H. / Mortenson, D.E. / Satyshur, K.A. / Forest, K.T. / Gellman, S.H.
History
DepositionOct 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Sep 20, 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_ncs_dom_lim
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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / 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.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GCN4pLI(alpha/beta/acyclic gamma)
B: GCN4pLI(alpha/beta/acyclic gamma)


Theoretical massNumber of molelcules
Total (without water)7,9962
Polymers7,9962
Non-polymers00
Water43224
1
A: GCN4pLI(alpha/beta/acyclic gamma)
B: GCN4pLI(alpha/beta/acyclic gamma)

A: GCN4pLI(alpha/beta/acyclic gamma)
B: GCN4pLI(alpha/beta/acyclic gamma)


Theoretical massNumber of molelcules
Total (without water)15,9914
Polymers15,9914
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7470 Å2
ΔGint-73 kcal/mol
Surface area7340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.920, 51.490, 31.030
Angle α, β, γ (deg.)90.000, 128.870, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLEULEUAA2 - 142 - 14
21ARGARGLEULEUBB2 - 142 - 14
12GLUGLUARGARGAA22 - 3322 - 33
22GLUGLUARGARGBB22 - 3322 - 33

NCS ensembles :
ID
1
2
DetailsTetramer generated via symmetry mate at -x,y,-z+1

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Components

#1: Protein/peptide GCN4pLI(alpha/beta/acyclic gamma)


Mass: 3997.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Generated via solid-phase peptide synthesis.
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 1.88 Å3/Da / Density % sol: 34.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M NaOAc, 8% w/v PEG4000, cryoprotected by addition of 24% PEG4000 to mother liquor, precipitant solution combined 1+1 uL with peptide stock at 10 mg/mL, pH 4.6, VAPOR DIFFUSION, HANGING ...Details: 0.1 M NaOAc, 8% w/v PEG4000, cryoprotected by addition of 24% PEG4000 to mother liquor, precipitant solution combined 1+1 uL with peptide stock at 10 mg/mL, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 14, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→17.62 Å / Num. obs: 6350 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.72 % / Biso Wilson estimate: 28.775 Å2 / Rsym value: 0.034 / Net I/σ(I): 23.38
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured obsNum. unique allNum. unique obsRsym value% possible all
1.7-1.743.73.7617724774770.34698.8
1679446
1686452
1567418
1625434
1536410
1416374
1444385
1337356
1313348
1267337
1158311
1099293
1007272
882238
876236
759206
609165
491135
20157

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.7.0009refinement
PDB_EXTRACT3.11data extraction
EMBLMD-2data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GCL

1gcl


Resolution: 1.7→17.62 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0 / SU B: 7.468 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.341 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.295 298 4.7 %RANDOM
Rwork0.2506 ---
obs0.2525 6053 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.41 Å2 / Biso mean: 22.6426 Å2 / Biso min: 5.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.05 Å2
2---0.82 Å2-0 Å2
3---0.83 Å2
Refine analyzeLuzzati coordinate error obs: 0.111 Å
Refinement stepCycle: LAST / Resolution: 1.7→17.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms535 0 0 24 559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02552
X-RAY DIFFRACTIONr_bond_other_d0.0020.02417
X-RAY DIFFRACTIONr_angle_refined_deg0.9062.123737
X-RAY DIFFRACTIONr_angle_other_deg1.00431041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.184554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.19926.1921
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03815128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.932153
X-RAY DIFFRACTIONr_chiral_restr0.0480.290
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.018529
X-RAY DIFFRACTIONr_gen_planes_other0.0010.01784
X-RAY DIFFRACTIONr_rigid_bond_restr2.2093969
X-RAY DIFFRACTIONr_sphericity_free15.39856
X-RAY DIFFRACTIONr_sphericity_bonded4.8165981
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: LOCAL / Weight: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms
11A3930.32
12B3930.32
21A3430.27
22B3430.27
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 26 -
Rwork0.343 451 -
all-477 -
obs--100 %

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