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- PDB-7dmf: A de novo protein that rigidly extends the structure of tVHS-like... -

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Basic information

Entry
Database: PDB / ID: 7dmf
TitleA de novo protein that rigidly extends the structure of tVHS-like domain in tepsin with a new designed domain
ComponentsDesigned protein EXTD-3
KeywordsDE NOVO PROTEIN / all helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsXu, Y.
CitationJournal: Nature / Year: 2022
Title: A backbone-centred energy function of neural networks for protein design.
Authors: Huang, B. / Xu, Y. / Hu, X. / Liu, Y. / Liao, S. / Zhang, J. / Huang, C. / Hong, J. / Chen, Q. / Liu, H.
History
DepositionDec 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 23, 2022Group: Database references / Structure summary / Category: citation / citation_author / entity
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity.pdbx_description
Revision 1.3Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Mar 9, 2022Group: Refinement description / Category: software
Revision 1.5Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Designed protein EXTD-3


Theoretical massNumber of molelcules
Total (without water)21,1901
Polymers21,1901
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.727, 69.727, 79.291
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Designed protein EXTD-3


Mass: 21189.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 53.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 20% w/v Polyethylene glycol 3350, pH 7.0, 0.2M Potassium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 11185 / % possible obs: 100 % / Redundancy: 19.6 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.031 / Rrim(I) all: 0.14 / Χ2: 0.985 / Net I/σ(I): 4.1 / Num. measured all: 218738
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.2417.20.5665450.9430.140.5840.991100
2.24-2.2817.50.5655480.9430.1390.5821.121100
2.28-2.3218.20.4295660.9540.1030.4420.976100
2.32-2.3718.60.4115540.9670.0970.4221.014100
2.37-2.4218.60.3855490.9760.0920.3960.948100
2.42-2.4818.20.3425680.9750.0820.3520.983100
2.48-2.54190.3255460.9780.0760.3340.957100
2.54-2.6120.80.325540.9790.0720.3280.97100
2.61-2.6920.80.2945670.9870.0660.3021.078100
2.69-2.7720.90.2455540.990.0550.2510.982100
2.77-2.8720.70.2375490.9870.0530.2430.991100
2.87-2.9920.50.1965590.9930.0450.2010.972100
2.99-3.12200.1685560.9940.0380.1721.006100
3.12-3.2918.60.1455720.9960.0340.1491.009100
3.29-3.49210.1235710.9970.0270.1261.07100
3.49-3.7621.30.1095480.9970.0240.1121.055100
3.76-4.1420.70.0945600.9980.0210.0961.038100
4.14-4.7418.80.0785600.9980.0180.080.914100
4.74-5.9720.50.0845690.9960.0190.0860.868100
5.97-5019.10.0585900.9980.0140.0590.76199.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5wf2

5wf2


Resolution: 2.201→26.181 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2686 823 9.8 %
Rwork0.2319 7573 -
obs0.2357 8396 75.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.09 Å2 / Biso mean: 44.7049 Å2 / Biso min: 13.85 Å2
Refinement stepCycle: final / Resolution: 2.201→26.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1478 0 0 5 1483
Biso mean---17.72 -
Num. residues----189
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.201-2.33850.2986970.2398108164
2.3385-2.5190.32861260.2403109266
2.519-2.77220.27541150.235117870
2.7722-3.17280.26371500.2443129378
3.1728-3.99510.30461400.2429153090
3.9951-26.1810.23481950.2118139984
Refinement TLS params.Method: refined / Origin x: 14.4114 Å / Origin y: -25.95 Å / Origin z: 3.0185 Å
111213212223313233
T0.2657 Å2-0.0332 Å20.0082 Å2-0.2198 Å20.0117 Å2--0.2218 Å2
L1.8771 °2-0.4956 °20.6413 °2-0.6128 °2-0.3737 °2--0.8363 °2
S0.1169 Å °-0.0478 Å °-0.1763 Å °0.0396 Å °-0.0374 Å °-0.0162 Å °0.0968 Å °0.0691 Å °-0.0864 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 6 through 194)

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