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- PDB-5tpj: Crystal structure of a de novo designed protein with curved beta-sheet -

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Basic information

Entry
Database: PDB / ID: 5tpj
TitleCrystal structure of a de novo designed protein with curved beta-sheet
Componentsdenovo NTF2
KeywordsDE NOVO PROTEIN / de novo NTF2
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.101 Å
AuthorsBasanta, B. / Oberdorfer, G. / Marcos, E. / Chidyausiku, T.M. / Sankaran, B. / Baker, D.
Funding support United States, Spain, Austria, 4items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)HDTRA 1-11-1-0041 United States
European CommissionFP7-PEOPLE-2011-IOF 298976 Spain
European Commission332094 ASR-CompEnzDes FP7-PEOPLE-2012-IOF Austria
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
CitationJournal: Science / Year: 2017
Title: Principles for designing proteins with cavities formed by curved beta sheets.
Authors: Marcos, E. / Basanta, B. / Chidyausiku, T.M. / Tang, Y. / Oberdorfer, G. / Liu, G. / Swapna, G.V. / Guan, R. / Silva, D.A. / Dou, J. / Pereira, J.H. / Xiao, R. / Sankaran, B. / Zwart, P.H. / ...Authors: Marcos, E. / Basanta, B. / Chidyausiku, T.M. / Tang, Y. / Oberdorfer, G. / Liu, G. / Swapna, G.V. / Guan, R. / Silva, D.A. / Dou, J. / Pereira, J.H. / Xiao, R. / Sankaran, B. / Zwart, P.H. / Montelione, G.T. / Baker, D.
History
DepositionOct 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 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

Downloads & links

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Assembly

Deposited unit
A: denovo NTF2


Theoretical massNumber of molelcules
Total (without water)14,9271
Polymers14,9271
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.810, 49.810, 113.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein denovo NTF2


Mass: 14927.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M ammonium citrate dibasic and 30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→56.56 Å / Num. obs: 2927 / % possible obs: 100 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.7

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Processing

Software
NameVersionClassification
PHENIXdev_1616refinement
iMOSFLM7.1.0data reduction
Aimless0.2.8data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.101→45.586 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.87
RfactorNum. reflection% reflection
Rfree0.2648 269 9.34 %
Rwork0.2209 --
obs0.2251 2881 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.101→45.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms970 0 0 1 971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007988
X-RAY DIFFRACTIONf_angle_d0.9771340
X-RAY DIFFRACTIONf_dihedral_angle_d15.982359
X-RAY DIFFRACTIONf_chiral_restr0.038153
X-RAY DIFFRACTIONf_plane_restr0.004171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1008-3.90630.3091380.25371250X-RAY DIFFRACTION100
3.9063-45.59060.24161310.20711362X-RAY DIFFRACTION100

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