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- PDB-6ij1: Crystal structure of a protein from Actinoplanes -

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Basic information

Entry
Database: PDB / ID: 6ij1
TitleCrystal structure of a protein from Actinoplanes
ComponentsPrenylcyclase
KeywordsTRANSFERASE / prenyltransferase
Function / homologyACETATE ION / IMIDAZOLE / Prenylcyclase
Function and homology information
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.521 Å
AuthorsYang, Z.Z. / Zhang, L.L. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structure of TchmY from Actinoplanes teichomyceticus.
Authors: Yang, Z. / Zhang, L. / Yu, X. / Wu, S. / Yang, Y. / Hu, Y. / Li, Q. / Shang, N. / Guo, R.T. / Chen, C.C. / Dai, L. / Liu, W.
History
DepositionOct 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 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
A: Prenylcyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6555
Polymers37,3891
Non-polymers2664
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-0 kcal/mol
Surface area13530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.471, 73.471, 124.234
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-630-

HOH

21A-667-

HOH

31A-797-

HOH

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Components

#1: Protein Prenylcyclase


Mass: 37388.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria)
Gene: tchmY / Plasmid: pET-46EK/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1B1ESM0
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.75M K/Na Tartrate, 0.3M Imidazole pH 8.0, 0.4M Nac

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 26, 2017
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→25 Å / Num. obs: 59674 / % possible obs: 98.9 % / Redundancy: 8.9 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.024 / Rrim(I) all: 0.071 / Χ2: 1.216 / Net I/σ(I): 14.6 / Num. measured all: 533592
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.52-1.5770.50655250.8710.2030.5471.19893.1
1.57-1.649.10.40159090.9530.1390.4251.20599.1
1.64-1.719.20.28859160.9780.0990.3051.21299.4
1.71-1.89.20.19759370.9870.0680.2091.17799.4
1.8-1.919.20.14159400.9930.0490.1491.16799.6
1.91-2.069.20.11459960.9930.040.1211.38499.8
2.06-2.279.20.08959960.9950.0310.0941.42999.8
2.27-2.69.20.06260480.9980.0220.0661.03199.9
2.6-3.279.20.06661040.9970.0230.071.423100
3.27-258.80.04863030.9980.0170.0510.92599.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.521→23.718 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.53
RfactorNum. reflection% reflection
Rfree0.1753 1987 3.33 %
Rwork0.1595 --
obs0.1601 59642 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.78 Å2 / Biso mean: 22.7697 Å2 / Biso min: 11.13 Å2
Refinement stepCycle: final / Resolution: 1.521→23.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2553 0 19 338 2910
Biso mean--22.59 34.44 -
Num. residues----334
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5208-1.57520.21131960.20175327552393
1.5752-1.63820.22232020.17755708591099
1.6382-1.71270.20562030.17125711591499
1.7127-1.8030.19771990.16765741594099
1.803-1.91590.20212000.16157375937100
1.9159-2.06380.20192000.162457985998100
2.0638-2.27130.16891980.153657995997100
2.2713-2.59960.18812010.159158456046100
2.5996-3.27390.161960.158859006096100
3.2739-23.72060.15551920.15356089628199

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