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- PDB-7vqv: de novo design based on 1r26 -

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Basic information

Entry
Database: PDB / ID: 7vqv
Titlede novo design based on 1r26
Componentsde novo designed protein
KeywordsDE NOVO PROTEIN
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsZhang, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Comput Sci / Year: 2023
Title: Rotamer-free protein sequence design based on deep learning and self-consistency.
Authors: Zhang, L.
History
DepositionOct 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: de novo designed protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3463
Polymers13,1621
Non-polymers1842
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-0 kcal/mol
Surface area6960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.516, 50.458, 64.699
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein de novo designed protein


Mass: 13162.040 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1,4-Dioxane, bicine, PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 20876 / % possible obs: 99.9 % / Redundancy: 12.2 % / CC1/2: 0.996 / Net I/σ(I): 38.271
Reflection shellResolution: 1.53→1.56 Å / Num. unique obs: 982 / CC1/2: 0.899

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1r26

1r26


Resolution: 1.53→32.37 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.344 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1002 4.8 %RANDOM
Rwork0.1869 ---
obs0.1887 19823 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.27 Å2 / Biso mean: 29.006 Å2 / Biso min: 15.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0 Å2-0 Å2
2---1.04 Å20 Å2
3---1.28 Å2
Refinement stepCycle: final / Resolution: 1.53→32.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 12 65 999
Biso mean--48.59 38.93 -
Num. residues----115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.013953
X-RAY DIFFRACTIONr_bond_other_d0.0010.017929
X-RAY DIFFRACTIONr_angle_refined_deg1.8541.6391289
X-RAY DIFFRACTIONr_angle_other_deg1.4371.5832155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5125116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.26723.84652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72115176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.779156
X-RAY DIFFRACTIONr_chiral_restr0.1030.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02191
LS refinement shellResolution: 1.535→1.575 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 66 -
Rwork0.244 1327 -
all-1393 -
obs--92.93 %

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