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- PDB-5yvk: Crystal structure of a cyclase Famc1 from Fischerella ambigua UTE... -

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Basic information

Entry
Database: PDB / ID: 5yvk
TitleCrystal structure of a cyclase Famc1 from Fischerella ambigua UTEX 1903
Componentscyclase
KeywordsTRANSFERASE / prenyltransferase
Function / homology: / HpiC1 cyclase / metal ion binding / Chem-0HZ / 12-epi-hapalindole U synthase
Function and homology information
Biological speciesFischerella ambigua UTEX 1903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.292 Å
AuthorsHu, X.Y. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: The Crystal Structure of a Class of Cyclases that Catalyze the Cope Rearrangement
Authors: Chen, C.C. / Hu, X. / Tang, X. / Yang, Y. / Ko, T.P. / Gao, J. / Zheng, Y. / Huang, J.W. / Yu, Z. / Li, L. / Han, S. / Cai, N. / Zhang, Y. / Liu, W. / Guo, R.T.
History
DepositionNov 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 26, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Mar 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

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Assembly

Deposited unit
A: cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7944
Polymers24,4601
Non-polymers3343
Water5,332296
1
A: cyclase
hetero molecules

A: cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5898
Polymers48,9202
Non-polymers6696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_767-x+2,-x+y+1,-z+7/31
Buried area1800 Å2
ΔGint-30 kcal/mol
Surface area16410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.845, 54.845, 152.562
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein cyclase / AmbU4


Mass: 24460.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella ambigua UTEX 1903 (bacteria)
Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: V5TER4
#2: Chemical ChemComp-0HZ / amino({3-[(3S,8aS)-1,4-dioxooctahydropyrrolo[1,2-a]pyrazin-3-yl]propyl}amino)methaniminium / CI-4 / [cyclo-(l-Arg-d-Pro)]


Type: peptide-like / Mass: 254.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N5O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.71 Å3/Da / Density % sol: 54.58 % / Mosaicity: 0.616 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.0M sodium citrate, 0.1M Imidazole pH 8.0

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Data collection

DiffractionMean temperature: 100 K
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: 1.29→25 Å / Num. obs: 67572 / % possible obs: 99.6 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.016 / Rrim(I) all: 0.057 / Χ2: 1.562 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.29-1.346.80.53264910.930.2010.5710.46596.6
1.34-1.3910.80.49566360.9650.1570.520.496100
1.39-1.4512.60.37767080.980.1110.3930.546100
1.45-1.5312.90.26967180.990.0780.280.679100
1.53-1.6312.90.18166750.9940.0530.1890.884100
1.63-1.7512.90.12967620.9960.0380.1351.248100
1.75-1.9312.80.08967580.9980.0260.0931.845100
1.93-2.2112.40.0768210.9980.0210.0732.867100
2.21-2.7811.90.05568630.9990.0170.0583.159100
2.78-2511.60.03771400.9990.0110.0392.82499.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.292→24.137 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1874 1909 2.96 %
Rwork0.1655 --
obs0.1661 64567 95.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.292→24.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 20 296 1842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141591
X-RAY DIFFRACTIONf_angle_d1.3962178
X-RAY DIFFRACTIONf_dihedral_angle_d5.227905
X-RAY DIFFRACTIONf_chiral_restr0.117246
X-RAY DIFFRACTIONf_plane_restr0.011287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2916-1.33770.25121720.2185419X-RAY DIFFRACTION83
1.3377-1.39130.22351710.17915839X-RAY DIFFRACTION91
1.3913-1.45460.22581810.16016086X-RAY DIFFRACTION93
1.4546-1.53130.18741970.14796166X-RAY DIFFRACTION95
1.5313-1.62720.18411910.14296213X-RAY DIFFRACTION96
1.6272-1.75280.17651940.15456374X-RAY DIFFRACTION97
1.7528-1.92910.18391980.15586450X-RAY DIFFRACTION98
1.9291-2.20810.1772010.1556574X-RAY DIFFRACTION99
2.2081-2.78130.18742010.17636637X-RAY DIFFRACTION100
2.7813-24.14110.18612030.16966900X-RAY DIFFRACTION99

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