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- PDB-5jg9: Crystal structure of the de novo mini protein gEHEE_06 -

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Basic information

Entry
Database: PDB / ID: 5jg9
TitleCrystal structure of the de novo mini protein gEHEE_06
Componentsde novo design, hyper stable, disulfide-rich mini protein
KeywordsDE NOVO PROTEIN / de novo design of hyper stable / disulfide-rich
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsRupert, P.B. / Johnsen, W.A.
CitationJournal: Nature / Year: 2016
Title: Accurate de novo design of hyperstable constrained peptides.
Authors: Bhardwaj, G. / Mulligan, V.K. / Bahl, C.D. / Gilmore, J.M. / Harvey, P.J. / Cheneval, O. / Buchko, G.W. / Pulavarti, S.V. / Kaas, Q. / Eletsky, A. / Huang, P.S. / Johnsen, W.A. / Greisen, P. ...Authors: Bhardwaj, G. / Mulligan, V.K. / Bahl, C.D. / Gilmore, J.M. / Harvey, P.J. / Cheneval, O. / Buchko, G.W. / Pulavarti, S.V. / Kaas, Q. / Eletsky, A. / Huang, P.S. / Johnsen, W.A. / Greisen, P.J. / Rocklin, G.J. / Song, Y. / Linsky, T.W. / Watkins, A. / Rettie, S.A. / Xu, X. / Carter, L.P. / Bonneau, R. / Olson, J.M. / Coutsias, E. / Correnti, C.E. / Szyperski, T. / Craik, D.J. / Baker, D.
History
DepositionApr 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Structure summary
Revision 1.2Oct 26, 2016Group: Database references
Revision 1.3Nov 2, 2016Group: Database references
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: de novo design, hyper stable, disulfide-rich mini protein
B: de novo design, hyper stable, disulfide-rich mini protein
C: de novo design, hyper stable, disulfide-rich mini protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6585
Polymers17,5313
Non-polymers1282
Water1,22568
1
A: de novo design, hyper stable, disulfide-rich mini protein


Theoretical massNumber of molelcules
Total (without water)5,8441
Polymers5,8441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: de novo design, hyper stable, disulfide-rich mini protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8792
Polymers5,8441
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: de novo design, hyper stable, disulfide-rich mini protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9362
Polymers5,8441
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.920, 45.533, 49.704
Angle α, β, γ (deg.)90.00, 105.09, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

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
11SERSERARGARGAA0 - 442 - 46
21SERSERARGARGBB0 - 442 - 46
12SERSERARGARGAA0 - 442 - 46
22SERSERARGARGCC0 - 442 - 46
13GLYGLYCYSCYSBB-1 - 451 - 47
23GLYGLYCYSCYSCC-1 - 451 - 47

NCS ensembles :
ID
1
2
3

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Components

#1: Protein/peptide de novo design, hyper stable, disulfide-rich mini protein


Mass: 5843.565 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Homo sapiens (human)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Peg, buffer 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 8734 / % possible obs: 96.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 14.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→47.99 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.042 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.214 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25084 412 4.7 %RANDOM
Rwork0.20067 ---
obs0.20306 8310 96.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.892 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20.4 Å2
2--2.12 Å20 Å2
3----1.51 Å2
Refinement stepCycle: 1 / Resolution: 2.09→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1204 0 7 68 1279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191249
X-RAY DIFFRACTIONr_bond_other_d0.0120.021162
X-RAY DIFFRACTIONr_angle_refined_deg2.1991.961653
X-RAY DIFFRACTIONr_angle_other_deg2.07832657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92321.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01515268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0451532
X-RAY DIFFRACTIONr_chiral_restr0.1350.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021456
X-RAY DIFFRACTIONr_gen_planes_other0.010.02340
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5992.003563
X-RAY DIFFRACTIONr_mcbond_other1.5952.004562
X-RAY DIFFRACTIONr_mcangle_it2.3022.988700
X-RAY DIFFRACTIONr_mcangle_other2.3012.988701
X-RAY DIFFRACTIONr_scbond_it2.1222.382686
X-RAY DIFFRACTIONr_scbond_other2.1222.381686
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3453.461951
X-RAY DIFFRACTIONr_long_range_B_refined5.7415.7361357
X-RAY DIFFRACTIONr_long_range_B_other5.73815.7531358
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.18 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A4820
12B4820
21A4934
22C4934
31B4820
32C4820
LS refinement shellResolution: 2.093→2.147 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 37 -
Rwork0.215 499 -
obs--80.84 %
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)
110.7312-1.1532-3.41173.04660.12443.5315-0.08240.010.1013-0.0952-0.0753-0.4115-0.06480.08760.15770.0152-0.02720.00330.10810.03050.0681-5.168-10.0749-3.183
23.45530.6462-2.97751.3783-2.175711.47770.1180.159-0.2748-0.1828-0.0249-0.03970.2533-0.3724-0.09320.03930.0176-0.01540.1097-0.00490.0544-12.4749-27.736-11.232
38.96111.7585-5.24513.7624-2.23736.2766-0.1049-0.0399-0.020.02680.04980.0481-0.20590.04390.05520.04120.0202-0.00270.1007-0.00610.0041-21.2446-5.9396-16.3155
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 45
2X-RAY DIFFRACTION2B-1 - 45
3X-RAY DIFFRACTION3C-1 - 45

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