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- PDB-7vql: de novo designed based on 1r26 -

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Basic information

Entry
Database: PDB / ID: 7vql
Titlede novo designed based on 1r26
Componentsde novo designed protein
KeywordsDE NOVO PROTEIN / de nove design protein
Function / homologyAMMONIUM ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.3Oct 9, 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)13,1114
Polymers12,9831
Non-polymers1283
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-0 kcal/mol
Surface area7250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.651, 50.809, 65.627
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: 12982.883 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, BIS-Tris propane

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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: 1.75→50 Å / Num. obs: 14304 / % possible obs: 99.9 % / Redundancy: 12.1 % / CC1/2: 0.998 / Net I/σ(I): 38.41
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 699 / CC1/2: 0.868

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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: 1.75→34.58 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.815 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2641 659 4.6 %RANDOM
Rwork0.2158 ---
obs0.218 13602 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.34 Å2 / Biso mean: 43.773 Å2 / Biso min: 23.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å2-0 Å20 Å2
2---1.44 Å20 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 1.75→34.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms908 0 8 37 953
Biso mean--53.29 45.75 -
Num. residues----115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013927
X-RAY DIFFRACTIONr_bond_other_d0.0010.017917
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.6371255
X-RAY DIFFRACTIONr_angle_other_deg1.3491.5832127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67324.58348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.32415174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.494155
X-RAY DIFFRACTIONr_chiral_restr0.0870.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02174
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.361 47 -
Rwork0.314 971 -
obs--98.45 %

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