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- PDB-4kyz: Three-dimensional structure of triclinic form of de novo design i... -

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Basic information

Entry
Database: PDB / ID: 4kyz
TitleThree-dimensional structure of triclinic form of de novo design 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 / domain insertion
Function / homologyRibosomal protein S10 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.492 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. / Kornhaber, G. / Montelione, G.T. / Hunt, J.F. / Tong, L. / 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 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 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 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Designed protein OR327
B: Designed protein OR327
C: Designed protein OR327
D: Designed protein OR327


Theoretical massNumber of molelcules
Total (without water)79,3724
Polymers79,3724
Non-polymers00
Water3,045169
1
A: Designed protein OR327


Theoretical massNumber of molelcules
Total (without water)19,8431
Polymers19,8431
Non-polymers00
Water181
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
Water181
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
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Designed protein OR327


Theoretical massNumber of molelcules
Total (without water)19,8431
Polymers19,8431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.819, 55.402, 78.258
Angle α, β, γ (deg.)82.030, 80.340, 90.030
Int Tables number1
Space group name H-MP1
Detailsmonomer,19.75 kD,99.6%

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Components

#1: Protein
Designed protein OR327


Mass: 19842.973 Da / Num. of mol.: 4
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 8
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:0.1M NH4H2PO4 0.1M Tris PEG8K 20% , microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 12, 2013
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: 2.492→30 Å / Num. obs: 23740 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 15

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1269refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KY3

4ky3


Resolution: 2.492→29.457 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.789 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 28.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1187 5 %random
Rwork0.191 ---
obs0.195 23724 94.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.8 Å2 / Biso mean: 33.308 Å2 / Biso min: 11.46 Å2
Refinement stepCycle: LAST / Resolution: 2.492→29.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5352 0 0 169 5521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085412
X-RAY DIFFRACTIONf_angle_d1.0777284
X-RAY DIFFRACTIONf_chiral_restr0.071856
X-RAY DIFFRACTIONf_plane_restr0.004932
X-RAY DIFFRACTIONf_dihedral_angle_d15.1042060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.492-2.6050.3281330.2352527266084
2.605-2.7430.2851480.2232808295695
2.743-2.9140.2771500.2042848299895
2.914-3.1390.2921480.2212806295495
3.139-3.4550.2891470.2092802294994
3.455-3.9540.2621520.1912880303297
3.954-4.9770.2241540.1642930308499
4.977-29.4590.2241550.1752936309198

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