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- PDB-6a9f: Crystal structure of a cyclase from Fischerella sp. TAU in comple... -

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Basic information

Entry
Database: PDB / ID: 6a9f
TitleCrystal structure of a cyclase from Fischerella sp. TAU in complex with 4-(1H-Indol-3-yl)butan-2-one
Componentsaromatic prenyltransferase
KeywordsTRANSFERASE / prenyltransferase
Function / homology: / HpiC1 cyclase / metal ion binding / 4-(1~{H}-indol-3-yl)butan-2-one / FisC
Function and homology information
Biological speciesMastigocladus laminosus UTEX LB 1931 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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 13, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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
C: aromatic prenyltransferase
D: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,14017
Polymers96,4674
Non-polymers67313
Water10,287571
1
A: aromatic prenyltransferase
C: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4428
Polymers48,2342
Non-polymers2096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-41 kcal/mol
Surface area17060 Å2
MethodPISA
2
B: aromatic prenyltransferase
D: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6989
Polymers48,2342
Non-polymers4647
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-37 kcal/mol
Surface area17020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.729, 53.285, 94.882
Angle α, β, γ (deg.)104.56, 91.14, 94.16
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
aromatic prenyltransferase


Mass: 24116.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mastigocladus laminosus UTEX LB 1931 (bacteria)
Strain: UTEX LB 1931 / Gene: fisC / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1P8VSL7

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Non-polymers , 5 types, 584 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-9BF / 4-(1~{H}-indol-3-yl)butan-2-one


Mass: 187.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13NO
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / 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: 2.01 Å3/Da / Density % sol: 38.77 % / Mosaicity: 0.966 °
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: May 19, 2018
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 80126 / % possible obs: 96.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.028 / Rrim(I) all: 0.05 / Χ2: 1.463 / Net I/σ(I): 15.6 / Num. measured all: 237170
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.813.20.53472960.8790.350.641.32495.6
1.81-1.893.30.36572740.9490.2390.4371.34995.9
1.89-1.973.30.23673090.9770.1540.2831.38696.1
1.97-2.073.30.16273180.9870.1060.1941.45296.5
2.07-2.23.20.11773280.9920.0770.1411.43896.6
2.2-2.373.20.08873410.9950.0580.1061.4896.8
2.37-2.613.20.06273390.9960.0410.0751.47297
2.61-2.993.20.04174040.9980.0270.0491.53597.3
2.99-3.773.20.02773750.9990.0180.0331.48897.4
3.77-253.20.02773480.9980.0180.0331.7196.7

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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: 1.7→23.92 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.73 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21083 3848 4.8 %RANDOM
Rwork0.18755 ---
obs0.18871 76132 96.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.088 Å2
Baniso -1Baniso -2Baniso -3
1-3.53 Å2-0.48 Å20.19 Å2
2---0.51 Å2-0.2 Å2
3----2.5 Å2
Refinement stepCycle: 1 / Resolution: 1.7→23.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6111 0 31 571 6713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0146350
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175569
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.678579
X-RAY DIFFRACTIONr_angle_other_deg0.9241.63713052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5115793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.57523.775302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75215933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5761524
X-RAY DIFFRACTIONr_chiral_restr0.0740.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027121
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021155
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_it3.0083.1633215
X-RAY DIFFRACTIONr_mcbond_other3.0083.1623213
X-RAY DIFFRACTIONr_mcangle_it4.0894.7313975
X-RAY DIFFRACTIONr_mcangle_other4.0884.7313976
X-RAY DIFFRACTIONr_scbond_it3.7243.5773135
X-RAY DIFFRACTIONr_scbond_other3.713.5773134
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.495.2224605
X-RAY DIFFRACTIONr_long_range_B_refined7.62762.81730633
X-RAY DIFFRACTIONr_long_range_B_other7.62562.80230553
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 248 -
Rwork0.337 5504 -
obs--94.47 %

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