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- PDB-4hjb: GCN4pLI derivative with alpha/beta/cyclic-gamma amino acid substi... -

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Basic information

Entry
Database: PDB / ID: 4hjb
TitleGCN4pLI derivative with alpha/beta/cyclic-gamma amino acid substitution pattern
ComponentsGCN4pLI(alpha/beta/cyclic-gamma)
KeywordsUNKNOWN FUNCTION / alpha/beta/gamma amino acid
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
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 / 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 / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 9, 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
C: GCN4pLI(alpha/beta/cyclic-gamma)
A: GCN4pLI(alpha/beta/cyclic-gamma)
B: GCN4pLI(alpha/beta/cyclic-gamma)
D: GCN4pLI(alpha/beta/cyclic-gamma)


Theoretical massNumber of molelcules
Total (without water)15,9714
Polymers15,9714
Non-polymers00
Water1,31573
1
C: GCN4pLI(alpha/beta/cyclic-gamma)
A: GCN4pLI(alpha/beta/cyclic-gamma)

C: GCN4pLI(alpha/beta/cyclic-gamma)
A: GCN4pLI(alpha/beta/cyclic-gamma)


Theoretical massNumber of molelcules
Total (without water)15,9714
Polymers15,9714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area6670 Å2
ΔGint-70 kcal/mol
Surface area6960 Å2
MethodPISA
2
B: GCN4pLI(alpha/beta/cyclic-gamma)
D: GCN4pLI(alpha/beta/cyclic-gamma)

B: GCN4pLI(alpha/beta/cyclic-gamma)
D: GCN4pLI(alpha/beta/cyclic-gamma)


Theoretical massNumber of molelcules
Total (without water)15,9714
Polymers15,9714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area6740 Å2
ΔGint-62 kcal/mol
Surface area7130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.190, 46.290, 34.880
Angle α, β, γ (deg.)90.000, 91.270, 90.000
Int Tables number3
Space group name H-MP121
DetailsTetramer generated with symmetry mate at -x,y,-z+1

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Components

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


Mass: 3992.791 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Generated via solid-phase peptide synthesis.
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.73 Å3/Da / Density % sol: 28.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Precipitant solution contained 0.2 M NaCl, 0.1 M NaOAc, 30% w/v MPD, 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: Apr 27, 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: 1.25→46.3 Å / Num. all: 27036 / Num. obs: 27036 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.34 % / Biso Wilson estimate: 12.9 Å2 / Rsym value: 0.05 / Net I/σ(I): 28.84
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 1.79 % / Mean I/σ(I) obs: 4.05 / Num. unique all: 1056 / Rsym value: 0.324 / % possible all: 47.5

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Processing

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

1gcl


Resolution: 1.25→46.29 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.303 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1914 1346 5 %RANDOM
Rwork0.1392 ---
obs0.1419 27035 89.07 %-
all-27035 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 176.59 Å2 / Biso mean: 20.9573 Å2 / Biso min: 9.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å2-0.23 Å2
2--0.3 Å20 Å2
3----0.05 Å2
Refine analyzeLuzzati coordinate error obs: 0.044 Å
Refinement stepCycle: LAST / Resolution: 1.25→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 0 0 73 1097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021082
X-RAY DIFFRACTIONr_bond_other_d0.0010.02802
X-RAY DIFFRACTIONr_angle_refined_deg2.892.1321456
X-RAY DIFFRACTIONr_angle_other_deg1.21532011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3895101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51526.58541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12415238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.584153
X-RAY DIFFRACTIONr_chiral_restr0.1350.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0181057
X-RAY DIFFRACTIONr_gen_planes_other0.0010.018159
X-RAY DIFFRACTIONr_rigid_bond_restr7.55831884
X-RAY DIFFRACTIONr_sphericity_free47.809532
X-RAY DIFFRACTIONr_sphericity_bonded24.89951903
LS refinement shellResolution: 1.248→1.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 42 -
Rwork0.166 1014 -
all-1056 -
obs--47.5 %

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