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- PDB-5tuj: Ancestral Cationic Amino Acid Solute Binding Protein (AncCDT-1) -

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Basic information

Entry
Database: PDB / ID: 5tuj
TitleAncestral Cationic Amino Acid Solute Binding Protein (AncCDT-1)
ComponentsAncestral protein CDT-Anc1
KeywordsSolute Binding Protein / periplasmic solute binding protein
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.352 Å
AuthorsKaczmarski, J.A. / Clifton, B.E. / Carr, P.D. / Jackson, C.J.
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein.
Authors: Clifton, B.E. / Kaczmarski, J.A. / Carr, P.D. / Gerth, M.L. / Tokuriki, N. / Jackson, C.J.
History
DepositionNov 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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

Downloads & links

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Assembly

Deposited unit
C: Ancestral protein CDT-Anc1


Theoretical massNumber of molelcules
Total (without water)26,2921
Polymers26,2921
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11310 Å2
Unit cell
Length a, b, c (Å)71.641, 71.641, 124.001
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ancestral protein CDT-Anc1


Mass: 26292.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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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: 3.49 Å3/Da / Density % sol: 64.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8 / Details: 0.2 M Lithium sulfate 0.1 M Tris 22.5 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.35→35.82 Å / Num. obs: 5646 / % possible obs: 99.8 % / Redundancy: 9.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.215 / Net I/σ(I): 8
Reflection shellResolution: 3.35→3.62 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.001 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.744 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.352→27.743 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3375 294 5.25 %
Rwork0.3049 --
obs0.3066 5601 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.352→27.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1738 0 0 0 1738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021776
X-RAY DIFFRACTIONf_angle_d0.5842417
X-RAY DIFFRACTIONf_dihedral_angle_d11.675624
X-RAY DIFFRACTIONf_chiral_restr0.02277
X-RAY DIFFRACTIONf_plane_restr0.003311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3516-4.22030.41651320.35432613X-RAY DIFFRACTION100
4.2203-27.74370.31061620.28162694X-RAY DIFFRACTION100
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)
13.425-2.6021-0.52685.3524-2.33644.54880.01621.21170.3401-0.75250.34720.42910.0777-1.34370.70110.67710.0348-0.03430.9770.01660.9173-40.11521.384436.3684
28.0827-0.47151.11243.3691-2.9586.1705-0.53930.24791.15150.0270.44990.6998-0.9788-0.53470.16080.4995-0.07070.06520.64940.04240.8817-33.896224.217641.04
36.42682.4361.97913.6722-2.43574.2988-0.29940.61880.53690.064-0.7543-0.6967-1.10531.2599-0.22510.5497-0.20230.07251.12990.1450.9425-12.565924.982921.7071
47.573-3.44951.83283.3483-0.25113.83410.8646-0.25930.2693-0.1881-0.9884-0.1174-0.34490.558-0.1760.4332-0.2661-0.00891.0107-0.04710.6986-19.88523.696918.0082
55.52461.6785-1.02925.4465-3.81593.5747-0.16330.1578-0.003-0.50730.1043-0.38250.1798-0.501-0.17670.6892-0.04550.04560.38480.00350.8551-27.87314.839441.776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 14 through 47 )
2X-RAY DIFFRACTION2chain 'C' and (resid 48 through 106 )
3X-RAY DIFFRACTION3chain 'C' and (resid 107 through 151 )
4X-RAY DIFFRACTION4chain 'C' and (resid 152 through 201 )
5X-RAY DIFFRACTION5chain 'C' and (resid 202 through 246 )

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