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- PDB-5yvl: Crystal structure of a cyclase Hpiu5 from Fischerella sp. ATCC 43239 -

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Basic information

Entry
Database: PDB / ID: 5yvl
TitleCrystal structure of a cyclase Hpiu5 from Fischerella sp. ATCC 43239
Componentscyclase
KeywordsTRANSFERASE / prenyltransferase
Function / homologymetal ion binding / 12-epi-hapalindole C/U synthase
Function and homology information
Biological speciesFischerella sp. ATCC 43239 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.059 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 1.3Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cyclase
B: cyclase
C: cyclase
D: cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,78215
Polymers98,1004
Non-polymers68111
Water9,476526
1
A: cyclase
B: cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3317
Polymers49,0502
Non-polymers2805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-0 kcal/mol
Surface area16990 Å2
MethodPISA
2
C: cyclase
D: cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4518
Polymers49,0502
Non-polymers4016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-17 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.390, 114.311, 132.439
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 28 through 225)
21chain B
31(chain C and resid 28 through 225)
41(chain D and resid 28 through 225)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 28 - 225 / Label seq-ID: 26 - 223

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 28 through 225)AA
2chain BBB
3(chain C and resid 28 through 225)CC
4(chain D and resid 28 through 225)DD

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Components

#1: Protein
cyclase / HpiU5


Mass: 24525.115 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella sp. ATCC 43239 (bacteria) / Gene: hpiU5 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A076NBW8
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.41 Å3/Da / Density % sol: 48.9 % / Mosaicity: 1.047 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2M sodium chloride, 20%(w/v) PEG4000

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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: Nov 15, 2017
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.059→25 Å / Num. obs: 56433 / % possible obs: 95 % / Redundancy: 4.1 % / Biso Wilson estimate: 33.47 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.024 / Rrim(I) all: 0.053 / Χ2: 1.294 / Net I/σ(I): 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.06-2.133.60.48355080.8310.2880.5661.28194.1
2.13-2.223.70.39254510.8860.230.4571.28692.9
2.22-2.323.70.31553820.9290.1820.3661.31691.8
2.32-2.443.80.2353450.970.130.2661.39591.1
2.44-2.593.80.16854060.9810.0950.1941.45791.6
2.59-2.83.90.11855510.9890.0660.1361.35694.2
2.8-3.084.30.06756750.9970.0350.0761.26195.7
3.08-3.524.60.04958650.9980.0240.0551.74298.3
3.52-4.434.80.02860170.9990.0130.0311.242100
4.43-254.60.018623310.0090.020.72599.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YVK

5yvk


Resolution: 2.059→24.993 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.12
RfactorNum. reflection% reflection
Rfree0.2361 1997 3.54 %
Rwork0.1789 --
obs0.1809 56358 94.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.93 Å2 / Biso mean: 38.2123 Å2 / Biso min: 20.03 Å2
Refinement stepCycle: final / Resolution: 2.059→24.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6205 0 68 526 6799
Biso mean--53.3 42.57 -
Num. residues----803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146383
X-RAY DIFFRACTIONf_angle_d1.4978721
X-RAY DIFFRACTIONf_chiral_restr0.084971
X-RAY DIFFRACTIONf_plane_restr0.0121157
X-RAY DIFFRACTIONf_dihedral_angle_d11.0623713
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3696X-RAY DIFFRACTION10.4TORSIONAL
12B3696X-RAY DIFFRACTION10.4TORSIONAL
13C3696X-RAY DIFFRACTION10.4TORSIONAL
14D3696X-RAY DIFFRACTION10.4TORSIONAL
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 (%)
2.0591-2.13260.27481940.24265274546893
2.1326-2.2180.31991930.23465256544993
2.218-2.31880.30281910.22445188537992
2.3188-2.4410.30951890.21275153534291
2.441-2.59380.23731920.19195220541292
2.5938-2.79380.29671960.21025346554294
2.7938-3.07450.24852010.19865470567196
3.0745-3.51830.24312070.18055659586698
3.5183-4.42870.20322130.1558006013100
4.4287-24.99440.19452210.153359956216100

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