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- PDB-7vqw: de novo designed protein based on 1r26 -

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Basic information

Entry
Database: PDB / ID: 7vqw
Titlede novo designed protein based on 1r26
Componentsde novo designed protein
KeywordsDE NOVO PROTEIN
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 / Refinement description / Category: citation / struct_ncs_dom_lim
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: de novo designed protein
B: de novo designed protein


Theoretical massNumber of molelcules
Total (without water)26,3462
Polymers26,3462
Non-polymers00
Water1629
1
A: de novo designed protein


Theoretical massNumber of molelcules
Total (without water)13,1731
Polymers13,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: de novo designed protein


Theoretical massNumber of molelcules
Total (without water)13,1731
Polymers13,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.743, 50.458, 65.112
Angle α, β, γ (deg.)90.000, 94.490, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 1 - 116 / Label seq-ID: 1 - 116

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein de novo designed protein


Mass: 13173.204 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 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: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 7778 / % possible obs: 96 % / Redundancy: 3.3 % / CC1/2: 0.994 / Net I/σ(I): 12.515
Reflection shellResolution: 2.45→2.49 Å / Num. unique obs: 680 / CC1/2: 0.848

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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: 2.45→39.87 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.925 / SU B: 13.151 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.284 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 505 6.1 %RANDOM
Rwork0.2184 ---
obs0.221 7778 95.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.39 Å2 / Biso mean: 55.225 Å2 / Biso min: 28.75 Å2
Baniso -1Baniso -2Baniso -3
1-5.68 Å20 Å21.26 Å2
2---4.04 Å2-0 Å2
3----1.81 Å2
Refinement stepCycle: final / Resolution: 2.45→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 0 9 1855
Biso mean---46.9 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131886
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171855
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.6342557
X-RAY DIFFRACTIONr_angle_other_deg1.5011.5884325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1985232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.29326.04786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.1615361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.739154
X-RAY DIFFRACTIONr_chiral_restr0.1110.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022049
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02343
Refine LS restraints NCS

Ens-ID: 1 / Number: 3177 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.21 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.452→2.515 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 31 -
Rwork0.323 492 -
all-523 -
obs--82.36 %

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