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- PDB-6iev: Crystal structure of a designed protein -

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Basic information

Entry
Database: PDB / ID: 6iev
TitleCrystal structure of a designed protein
ComponentsDesigned protein
KeywordsSTRUCTURAL PROTEIN / Thioredoxin / Enzyme / Folded / designed
Function / homologyGlutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHan, M. / Liao, S. / Chen, Q. / Liu, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaU1732156 China
National Natural Science Foundation of China31470717 China
CitationJournal: Protein Sci. / Year: 2019
Title: Selection and analyses of variants of a designed protein suggest importance of hydrophobicity of partially buried sidechains for protein stability at high temperatures.
Authors: Han, M. / Liao, S. / Peng, X. / Zhou, X. / Chen, Q. / Liu, H.
History
DepositionSep 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Designed protein
B: Designed protein
C: Designed protein


Theoretical massNumber of molelcules
Total (without water)43,3273
Polymers43,3273
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-7 kcal/mol
Surface area16760 Å2
Unit cell
Length a, b, c (Å)124.855, 124.855, 58.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Designed protein


Mass: 14442.325 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Enterobacteria phage L1 (virus)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M Potassium sodium tartrate, 0.1M Sodium citrate pH5.6, 2.0MAmmonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.25→124.86 Å / Num. obs: 22476 / % possible obs: 99.8 % / Redundancy: 27.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.023 / Rrim(I) all: 0.12 / Net I/av σ(I): 21.8 / Net I/σ(I): 21.8
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 28.9 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 6.9 / Num. unique obs: 1628 / CC1/2: 0.977 / Rpim(I) all: 0.125 / Rrim(I) all: 0.675 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R26

1r26


Resolution: 2.25→44.143 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.39 / Phase error: 25.28
RfactorNum. reflection% reflection
Rfree0.2314 1149 5.13 %
Rwork0.1927 --
obs0.1947 22418 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→44.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2533 0 0 83 2616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012578
X-RAY DIFFRACTIONf_angle_d1.5393501
X-RAY DIFFRACTIONf_dihedral_angle_d9.41614
X-RAY DIFFRACTIONf_chiral_restr0.077416
X-RAY DIFFRACTIONf_plane_restr0.01450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2503-2.35270.30041380.25482617X-RAY DIFFRACTION100
2.3527-2.47670.29831390.23222604X-RAY DIFFRACTION100
2.4767-2.63180.28651350.22512635X-RAY DIFFRACTION100
2.6318-2.8350.32371320.23632631X-RAY DIFFRACTION100
2.835-3.12020.29851440.21142662X-RAY DIFFRACTION100
3.1202-3.57160.21281540.18762647X-RAY DIFFRACTION100
3.5716-4.49910.1881360.16962713X-RAY DIFFRACTION100
4.4991-44.15140.20481710.17432760X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 31.4312 Å / Origin y: 6.2188 Å / Origin z: 5.6131 Å
111213212223313233
T0.2909 Å2-0.0143 Å2-0.0269 Å2-0.2834 Å20.0072 Å2--0.2905 Å2
L1.0101 °2-0.3519 °20.3227 °2-0.3587 °20.289 °2--0.4318 °2
S0.0004 Å °0.171 Å °-0.0398 Å °-0.0688 Å °-0.0443 Å °0.0149 Å °0.0854 Å °-0.0822 Å °0.0462 Å °
Refinement TLS groupSelection details: all

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