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- PDB-5ts4: Crystal structure of a de novo designed protein with curved beta-sheet -

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Basic information

Entry
Database: PDB / ID: 5ts4
TitleCrystal structure of a de novo designed protein with curved beta-sheet
Componentsdenovo NTF2
KeywordsDE NOVO PROTEIN / de novo NTF2
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.005 Å
AuthorsBasanta, B. / Oberdorfer, G. / Chidyausiku, T.M. / Marcos, E. / Pereira, J.H. / Sankaran, B. / Zwart, P.H. / 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 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: denovo NTF2
B: denovo NTF2
C: denovo NTF2
D: denovo NTF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2195
Polymers53,1124
Non-polymers1061
Water41423
1
A: denovo NTF2


Theoretical massNumber of molelcules
Total (without water)13,2781
Polymers13,2781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: denovo NTF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3842
Polymers13,2781
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: denovo NTF2


Theoretical massNumber of molelcules
Total (without water)13,2781
Polymers13,2781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: denovo NTF2


Theoretical massNumber of molelcules
Total (without water)13,2781
Polymers13,2781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.307, 101.538, 101.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
denovo NTF2


Mass: 13278.111 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.03 Å3/Da / Density % sol: 39.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris hydrochloride, pH 8.5 and 25% PEG 3,350

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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: Oct 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→40.65 Å / Num. obs: 8652 / % possible obs: 98 % / Redundancy: 8 % / Net I/σ(I): 16

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Processing

Software
NameVersionClassification
PHENIXdev_1616refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.005→40.65 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.36
RfactorNum. reflection% reflection
Rfree0.3162 819 9.79 %
Rwork0.2741 --
obs0.278 8365 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.005→40.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2814 0 7 23 2844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062858
X-RAY DIFFRACTIONf_angle_d0.7193814
X-RAY DIFFRACTIONf_dihedral_angle_d12.351994
X-RAY DIFFRACTIONf_chiral_restr0.032401
X-RAY DIFFRACTIONf_plane_restr0.003516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0052-3.19350.4481180.40281080X-RAY DIFFRACTION86
3.1935-3.43990.44221420.33211256X-RAY DIFFRACTION98
3.4399-3.78590.34571440.31961258X-RAY DIFFRACTION99
3.7859-4.33320.31851410.28841290X-RAY DIFFRACTION100
4.3332-5.45720.29641440.23341283X-RAY DIFFRACTION99
5.4572-40.65720.26791300.25111379X-RAY DIFFRACTION99

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