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- PDB-6a99: Crystal structure of a Stig cyclases Fisc from Fischerella sp. TA... -

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Basic information

Entry
Database: PDB / ID: 6a99
TitleCrystal structure of a Stig cyclases Fisc from Fischerella sp. TAU in complex with (3Z)-3-(1-methyl-2-pyrrolidinylidene)-3H-indole
Componentsaromatic prenyltransferase
KeywordsTRANSFERASE / prenyltransferase
Function / homology: / HpiC1 cyclase / metal ion binding / (3~{Z})-3-(1-methylpyrrolidin-2-ylidene)indole / FisC
Function and homology information
Biological speciesFischerella sp. UTEX 'LB 1931' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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 12, 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
C: aromatic prenyltransferase
D: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,85220
Polymers96,4674
Non-polymers1,38516
Water3,027168
1
A: aromatic prenyltransferase
B: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,23612
Polymers48,2342
Non-polymers1,00210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-42 kcal/mol
Surface area16370 Å2
MethodPISA
2
D: aromatic prenyltransferase
hetero molecules

C: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6168
Polymers48,2342
Non-polymers3836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area2090 Å2
ΔGint-38 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.454, 82.398, 136.575
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
aromatic prenyltransferase


Mass: 24116.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella sp. UTEX 'LB 1931' (bacteria)
Gene: fisC / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1P8VSL7
#2: Chemical
ChemComp-9UL / (3~{Z})-3-(1-methylpyrrolidin-2-ylidene)indole


Mass: 198.264 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C13H14N2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.05 Å3/Da / Density % sol: 40.13 %
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: 2.29→25 Å / Num. obs: 36512 / % possible obs: 99.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.035 / Rrim(I) all: 0.074 / Χ2: 1.336 / Net I/σ(I): 12.5 / Num. measured all: 147545
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.32-2.43.90.42233540.8590.2410.4870.50998.3
2.4-2.54.30.35934130.910.1930.4080.52199.9
2.5-2.614.40.27534170.9440.1470.3120.552100
2.61-2.754.40.20134300.9680.1080.2290.7199.9
2.75-2.924.40.13534380.9870.0730.1540.671100
2.92-3.154.40.08434390.9940.0450.0960.845100
3.15-3.464.30.05534690.9970.030.0631.071100
3.46-3.964.30.04634840.9970.0250.0531.05799.9
3.96-4.994.20.05435190.9950.030.0621.9999.9
4.99-2540.04936830.9930.0270.0575.4399.6

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Processing

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

5yvk


Resolution: 2.29→24.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.353 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 1770 4.9 %RANDOM
Rwork0.18738 ---
obs0.19005 34521 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.838 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å20 Å2
2--1.31 Å2-0 Å2
3----2.49 Å2
Refinement stepCycle: 1 / Resolution: 2.29→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6108 0 86 168 6362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0146400
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175607
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.6848667
X-RAY DIFFRACTIONr_angle_other_deg0.8161.64913139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1995793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.65423.795303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.73515933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.8641524
X-RAY DIFFRACTIONr_chiral_restr0.0610.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027181
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021174
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_it3.6525.0983213
X-RAY DIFFRACTIONr_mcbond_other3.6485.0973211
X-RAY DIFFRACTIONr_mcangle_it5.337.6323975
X-RAY DIFFRACTIONr_mcangle_other5.3317.6333976
X-RAY DIFFRACTIONr_scbond_it4.145.5933187
X-RAY DIFFRACTIONr_scbond_other4.1375.5893185
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3028.2164692
X-RAY DIFFRACTIONr_long_range_B_refined9.53697.29727351
X-RAY DIFFRACTIONr_long_range_B_other9.53697.29727344
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.349 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 119 -
Rwork0.284 2387 -
obs--94.67 %

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