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- PDB-5l33: Crystal structure of a de novo designed protein with curved beta-sheet -

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Basic information

Entry
Database: PDB / ID: 5l33
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: 2 Å
AuthorsOberdorfer, G. / Marcos, E. / Basanta, B. / Chidyausiku, T.M. / Sankaran, B. / Baker, D.
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
DepositionAug 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Mar 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

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Assembly

Deposited unit
A: denovo NTF2


Theoretical massNumber of molelcules
Total (without water)12,8471
Polymers12,8471
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.250, 34.360, 100.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein denovo NTF2


Mass: 12847.328 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


Mass: 18.015 Da / Num. of mol.: 69 / 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: 1.92 Å3/Da / Density % sol: 35.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium MOPS/HEPES, pH 7.5, 12.5% PEG 1000, 12.5% PEG 3350 and 12.5% 2-methyl-2,4-pentanediol and 0.2 M of amino acids (sodium glutamate, DL-alanine, glycine, DL-lysine HCl and DL-serine)

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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: Jan 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50.195 Å / Num. obs: 6503 / % possible obs: 92.3 % / Redundancy: 7.8 % / Net I/σ(I): 24.6

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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: 2→50.195 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.52
RfactorNum. reflection% reflection
Rfree0.2013 307 4.72 %
Rwork0.1723 --
obs0.1737 6503 92.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→50.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms893 0 0 69 962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007937
X-RAY DIFFRACTIONf_angle_d0.8751265
X-RAY DIFFRACTIONf_dihedral_angle_d17.211371
X-RAY DIFFRACTIONf_chiral_restr0.037130
X-RAY DIFFRACTIONf_plane_restr0.003171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.51990.24331560.19222920X-RAY DIFFRACTION90
2.5199-50.21080.18511510.16533276X-RAY DIFFRACTION94
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)
10.01060.00290.22370.33840.45970.7953-0.0278-0.3008-0.134-0.1052-0.0288-0.27020.03840.80990.01520.09950.03670.04250.28820.01310.193127.591511.590463.3732
20.1192-0.0803-0.14350.3572-0.20970.23020.44810.0666-0.14640.70420.02090.338-0.7604-0.03280.04330.0006-0.0064-0.03410.2225-0.09120.213815.790315.207870.22
30.76060.48020.39390.64340.97820.72460.1883-0.20820.01730.124-0.1681-0.06070.2345-0.0010.01960.19470.02950.03470.14210.00640.125917.34457.882264.1183
40.33880.1611-0.07250.2891-0.69911.27520.141-0.10060.0162-0.1355-0.15340.008-0.2327-0.221-0.00320.16690.02310.01270.1174-0.00510.15515.887613.754259.3635
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 36 )
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 66 )
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 104 )

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