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- PDB-6w90: De novo designed NTF2 fold protein NT-9 -

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Basic information

Entry
Database: PDB / ID: 6w90
TitleDe novo designed NTF2 fold protein NT-9
ComponentsNTF2 fold protein loop-helix-loop design NT-9
KeywordsDE NOVO PROTEIN / protein design / de novo fold family / loop-helix-loop motif / geometric sampling
Function / homology1,2-Distearoyl-sn-glycerophosphoethanolamine
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsThompson, M.C. / Pan, X. / Liu, L. / Fraser, J.S. / Kortemme, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM110089 United States
CitationJournal: Science / Year: 2020
Title: Expanding the space of protein geometries by computational design of de novo fold families.
Authors: Pan, X. / Thompson, M.C. / Zhang, Y. / Liu, L. / Fraser, J.S. / Kelly, M.J.S. / Kortemme, T.
History
DepositionMar 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Mar 6, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NTF2 fold protein loop-helix-loop design NT-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5302
Polymers15,7821
Non-polymers7481
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.500, 51.990, 66.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein NTF2 fold protein loop-helix-loop design NT-9


Mass: 15781.833 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-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.83 Å3/Da / Density % sol: 32.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES Buffer, 30% PEG-600, 5% PEG-1000, 10% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 22, 2019
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.5→40.94 Å / Num. obs: 19203 / % possible obs: 99.9 % / Redundancy: 22.7 % / Biso Wilson estimate: 24.17 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.019 / Net I/σ(I): 18.5
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 895 / CC1/2: 0.719 / Rpim(I) all: 0.283

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: design model

Resolution: 1.5→40.94 Å / SU ML: 0.176 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.4663
RfactorNum. reflection% reflection
Rfree0.2104 997 5.21 %
Rwork0.1864 --
obs0.1876 19151 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.81 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 48 61 1217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01341313
X-RAY DIFFRACTIONf_angle_d1.31031774
X-RAY DIFFRACTIONf_chiral_restr0.0729180
X-RAY DIFFRACTIONf_plane_restr0.008237
X-RAY DIFFRACTIONf_dihedral_angle_d21.4462827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.580.30231350.26122500X-RAY DIFFRACTION97.3
1.58-1.680.2451420.23462562X-RAY DIFFRACTION100
1.68-1.810.28751410.22422539X-RAY DIFFRACTION100
1.81-1.990.25051400.20152583X-RAY DIFFRACTION99.96
1.99-2.280.22551360.18432601X-RAY DIFFRACTION100
2.28-2.870.19331520.1952611X-RAY DIFFRACTION99.96
2.87-40.940.19211510.16982758X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.126276098510.286557926073-0.8870389655951.762893724670.1073689873951.1469764020.1349052756860.145976588416-0.2202326781890.272596076595-0.05625714162950.04711447619940.339207679836-0.19903604610.001045990106110.251220571687-0.009903978654560.006698089204820.235807408636-0.02550346975450.237948668217-3.46392072226-6.78034626521-6.00374714379
20.149376461201-0.279400208056-0.1271462345020.7547326731380.7630669436831.25550122609-0.0916724573632-0.1113459938910.1223300001190.56375703786-0.0117354652004-0.06728119389490.1228257543130.102730550497-0.00252975114090.2144866568970.0202383772397-0.003834122679910.1946236061640.00674898299810.211898211385-8.813853075747.85449350668-0.632840519123
30.9524216772780.813049299672-0.2580518807771.006305639090.1158132176010.417931583020.216513227740.3193941853310.0560028145963-0.092038965575-0.3713193072180.2252080665570.0509402350749-0.06000435703210.04431186728730.3132246416280.1090154034380.01565636536820.4791281481580.008429690785920.32136986385-13.20583317583.34679788434-11.5982751615
40.2903119039860.5269890439560.5363810302311.989116734620.7544895623951.040961400570.09613132743890.0230142853940.0961776078678-0.0332939659740.0562740290457-0.334290877309-0.2554638810070.2436893065540.001380663173450.1959289165930.0617397294404-0.02039776489330.2550677893450.001823517509250.2228772653924.907551489833.10967483639-8.11874944018
50.64760379143-0.441301987147-0.2208967175220.7205201720810.3221358406120.537963366962-0.080881174243-0.0202514300120.0764386543392-0.1188225128940.012959465005-0.2338442542760.293258561970.158589043611-0.005642508509010.2526325219760.0112581483159-0.04763149265280.2288434217920.02652426409280.23601282695-2.78018639227.79932427357-0.743033920608
60.5173964434580.138327386005-0.4387376578510.7119856721350.1608459174681.103467827390.2455380711360.3606363689170.304004022561-0.407729493118-0.03961786367040.385699957322-0.149857565698-0.5173953658340.01584986856190.235044302475-0.01874423487170.008573705596680.23339304728-0.009147146885580.254608828903-10.664450937615.6277676758-11.8667744837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 47 )
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 64 )
4X-RAY DIFFRACTION4chain 'A' and (resid 65 through 102 )
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 114 )
6X-RAY DIFFRACTION6chain 'A' and (resid 115 through 128 )

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