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- PDB-4ky3: Three-dimensional Structure of the orthorhombic crystal of comput... -

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Basic information

Entry
Database: PDB / ID: 4ky3
TitleThree-dimensional Structure of the orthorhombic crystal of computationally designed insertion domain , Northeast Structural Genomics Consortium (NESG) Target OR327
Componentsdesigned protein OR327
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyRibosomal protein S10 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.964 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Gleixner, J. / Baker, D. / Everett, J.K. / Acton, T.B. ...Kuzin, A. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Gleixner, J. / Baker, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Elife / Year: 2015
Title: Precise assembly of complex beta sheet topologies from de novo designed building blocks.
Authors: King, I.C. / Gleixner, J. / Doyle, L. / Kuzin, A. / Hunt, J.F. / Xiao, R. / Montelione, G.T. / Stoddard, B.L. / DiMaio, F. / Baker, D.
History
DepositionMay 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Feb 17, 2016Group: Database references
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: designed protein OR327
B: designed protein OR327
C: designed protein OR327


Theoretical massNumber of molelcules
Total (without water)59,5293
Polymers59,5293
Non-polymers00
Water00
1
A: designed protein OR327


Theoretical massNumber of molelcules
Total (without water)19,8431
Polymers19,8431
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: designed protein OR327


Theoretical massNumber of molelcules
Total (without water)19,8431
Polymers19,8431
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: designed protein OR327


Theoretical massNumber of molelcules
Total (without water)19,8431
Polymers19,8431
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.207, 71.850, 118.008
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsmonomer,19.75 kD,99.6%

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Components

#1: Protein designed protein OR327


Mass: 19842.973 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 277 K / pH: 4.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir 0.1M NaAcetate pH: 4.5 PEG 3350 25%(w/v) , microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 14, 2013 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.964→30 Å / Num. obs: 20480 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 74.71 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 23.7

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1269refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.964→28.156 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.52 / σ(F): 1.45 / Phase error: 31.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2711 1019 4.99 %
Rwork0.1867 --
obs0.1912 20441 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.731 Å2
Refinement stepCycle: LAST / Resolution: 2.964→28.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3839 0 0 0 3839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013878
X-RAY DIFFRACTIONf_angle_d1.3495220
X-RAY DIFFRACTIONf_dihedral_angle_d19.321489
X-RAY DIFFRACTIONf_chiral_restr0.086620
X-RAY DIFFRACTIONf_plane_restr0.004668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9644-3.12050.44631330.32322561X-RAY DIFFRACTION90
3.1205-3.31580.37981450.25792797X-RAY DIFFRACTION99
3.3158-3.57130.31480.23642827X-RAY DIFFRACTION99
3.5713-3.92990.31081510.19362817X-RAY DIFFRACTION100
3.9299-4.49650.24461520.16842824X-RAY DIFFRACTION100
4.4965-5.65760.23241440.15522812X-RAY DIFFRACTION100
5.6576-28.15710.2281460.15632784X-RAY DIFFRACTION98

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