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- PDB-6a8x: Crystal structure of a apo form cyclase from Fischerella sp. -

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Basic information

Entry
Database: PDB / ID: 6a8x
TitleCrystal structure of a apo form cyclase from Fischerella sp.
Componentsaromatic prenyltransferase
KeywordsTRANSPORT PROTEIN / prenyltransferase
Function / homologyHpiC1 cyclase / metal ion binding / 12-epi-fischeindole U synthase
Function and homology information
Biological speciesFischerella ambigua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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
DepositionJul 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: aromatic prenyltransferase
B: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6406
Polymers48,4802
Non-polymers1604
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-35 kcal/mol
Surface area17500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.993, 90.993, 234.496
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein aromatic prenyltransferase


Mass: 24239.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella ambigua (bacteria) / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1L1VVY8
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 220 / 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: 5.01 Å3/Da / Density % sol: 75.43 % / Mosaicity: 1.091 °
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: Jan 2, 2018
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→25 Å / Num. obs: 40767 / % possible obs: 96.8 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.028 / Rrim(I) all: 0.082 / Χ2: 1.916 / Net I/σ(I): 12.2 / Num. measured all: 362774
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.4310.10.70641210.8560.2310.7451.379100
2.43-2.5310.10.52941260.9150.1730.5581.462100
2.53-2.65100.38641290.9520.1270.4071.531100
2.65-2.799.90.28141390.9730.0930.2971.67499.8
2.79-2.969.70.18841510.9880.0630.1991.85499.6
2.96-3.199.30.12941330.9930.0440.1372.29499.1
3.19-3.518.50.07941230.9960.0290.0852.4697.8
3.51-4.017.50.05739860.9970.0220.0622.56794.5
4.01-5.055.70.04536170.9970.020.0492.84584
5.05-257.70.03242420.9990.0120.0351.9293.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YVK

5yvk


Resolution: 2.35→24.85 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.18 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 1959 4.8 %RANDOM
Rwork0.19506 ---
obs0.19692 38471 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.156 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0 Å2-0 Å2
2---0.89 Å20 Å2
3---1.78 Å2
Refinement stepCycle: 1 / Resolution: 2.35→24.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3088 0 4 220 3312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0143180
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172816
X-RAY DIFFRACTIONr_angle_refined_deg1.381.6634302
X-RAY DIFFRACTIONr_angle_other_deg0.861.6366602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9835404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12623.867150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.32815486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.351512
X-RAY DIFFRACTIONr_chiral_restr0.0630.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023592
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02576
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0735.2111636
X-RAY DIFFRACTIONr_mcbond_other5.0565.2081633
X-RAY DIFFRACTIONr_mcangle_it6.5397.792024
X-RAY DIFFRACTIONr_mcangle_other6.5387.7952025
X-RAY DIFFRACTIONr_scbond_it6.6445.7851544
X-RAY DIFFRACTIONr_scbond_other6.6425.7891545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.9118.4082279
X-RAY DIFFRACTIONr_long_range_B_refined10.24599.60213137
X-RAY DIFFRACTIONr_long_range_B_other10.25699.47113011
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 155 -
Rwork0.279 2858 -
obs--99.93 %

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