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- PDB-6jcc: structure of a de novo protein D_1CY5_M1 -

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Basic information

Entry
Database: PDB / ID: 6jcc
Titlestructure of a de novo protein D_1CY5_M1
ComponentsComputational designed protein based on evolution
KeywordsDE NOVO PROTEIN / designed protein evolution crystal structure helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsMeng, W. / Feng, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370755 China
CitationJournal: To Be Published
Title: structure of a computationally designed mutant protein D_1CY5_M1
Authors: Meng, W. / Haiyan, L.
History
DepositionJan 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Computational designed protein based on evolution


Theoretical massNumber of molelcules
Total (without water)11,0861
Polymers11,0861
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.321, 38.159, 64.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Computational designed protein based on evolution


Mass: 11085.901 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.95 Å3/Da / Density % sol: 36.92 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 15784 / % possible obs: 98.8 % / Redundancy: 7.9 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.023 / Rrim(I) all: 0.065 / Net I/av σ(I): 4.588 / Net I/σ(I): 29.37
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.422 / Num. unique obs: 1523 / Rpim(I) all: 0.159

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575-000refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.11.1-2575-000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→32.8 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20304 776 4.9 %Random
Rwork0.18605 ---
obs0.18689 14969 98.8 %-
Solvent computationBsol: 47.2 Å2 / ksol: 0.46 e/Å3
Displacement parametersBiso mean: 16.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--1.38 Å2-0 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.45→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms760 0 0 75 835
LS refinement shellResolution: 1.451→1.489 Å
RfactorNum. reflection% reflection
Rfree0.258 59 -
Rwork0.232 1071 -
obs--96.58 %

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