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- PDB-5yvp: Crystal structure of an apo form cyclase Filc1 from Fischerella s... -

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Basic information

Entry
Database: PDB / ID: 5yvp
TitleCrystal structure of an apo form cyclase Filc1 from Fischerella sp. TAU
Componentscyclase A
KeywordsTRANSFERASE / prenyltransferase
Function / homology: / HpiC1 cyclase / metal ion binding / 12-epi-hapalindole U synthase
Function and homology information
Biological speciesFischerella sp. TAU (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.051 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 27, 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 1.2Jan 2, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,39714
Polymers97,6884
Non-polymers70910
Water6,648369
1
A: cyclase A
C: cyclase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1997
Polymers48,8442
Non-polymers3555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-3 kcal/mol
Surface area17180 Å2
MethodPISA
2
B: cyclase A
D: cyclase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1997
Polymers48,8442
Non-polymers3555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-5 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.758, 255.893, 34.912
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-479-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 28 through 225)
21(chain B and resid 28 through 225)
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: THR / End label comp-ID: THR / 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
2(chain B and resid 28 through 225)BB
3chain CCC
4chain DDD

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Components

#1: Protein
cyclase A / FilC1


Mass: 24422.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella sp. TAU (bacteria) / Gene: filC1 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1P8VSI6
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 1.98 Å3/Da / Density % sol: 37.99 % / Mosaicity: 0.714 °
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 4, 2017
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. obs: 49655 / % possible obs: 99.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 33.44 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.038 / Rrim(I) all: 0.082 / Χ2: 1.935 / Net I/σ(I): 15.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.124.90.448560.9560.2010.4491.66299.9
2.12-2.214.90.31549180.9690.1570.3531.694100
2.21-2.314.90.2449410.9840.120.2691.796100
2.31-2.434.90.17949180.9890.0890.2011.887100
2.43-2.584.90.13249340.9920.0670.1482.00199.9
2.58-2.784.80.10749890.9940.0540.122.03899.7
2.78-3.064.80.07749570.9940.040.0882.16899.6
3.06-3.550.05750370.9960.0290.0642.09399.1
3.5-4.414.90.05549450.9950.0290.0632.01597.1
4.41-254.90.05251600.9940.0280.0591.98596.3

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Processing

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

5yvk


Resolution: 2.051→24.242 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.03
RfactorNum. reflection% reflection
Rfree0.255 1993 4.03 %
Rwork0.2123 --
obs0.214 49490 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.66 Å2 / Biso mean: 42.5092 Å2 / Biso min: 21.41 Å2
Refinement stepCycle: final / Resolution: 2.051→24.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6120 0 34 369 6523
Biso mean--64.55 45.13 -
Num. residues----794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076292
X-RAY DIFFRACTIONf_angle_d1.1098586
X-RAY DIFFRACTIONf_chiral_restr0.066966
X-RAY DIFFRACTIONf_plane_restr0.0061130
X-RAY DIFFRACTIONf_dihedral_angle_d9.9063654
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3681X-RAY DIFFRACTION13.062TORSIONAL
12B3681X-RAY DIFFRACTION13.062TORSIONAL
13C3681X-RAY DIFFRACTION13.062TORSIONAL
14D3681X-RAY DIFFRACTION13.062TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0508-2.1020.33921340.25853199333397
2.102-2.15880.32621450.251134123557100
2.1588-2.22230.31141400.245533513491100
2.2223-2.2940.30071420.241233543496100
2.294-2.37590.32341420.248533673509100
2.3759-2.47090.32581430.240834343577100
2.4709-2.58330.31991410.238533493490100
2.5833-2.71930.31251420.24534223564100
2.7193-2.88940.29391440.24063401354599
2.8894-3.11210.28271410.23563414355599
3.1121-3.42450.23671430.21763409355299
3.4245-3.91820.21621430.19533417356098
3.9182-4.92970.1981430.16493375351896
4.9297-24.24380.23361500.19663593374397
Refinement TLS params.Method: refined / Origin x: -21.8275 Å / Origin y: -14.6614 Å / Origin z: -8.4694 Å
111213212223313233
T0.2586 Å20.0116 Å20.0408 Å2-0.294 Å20.0159 Å2--0.275 Å2
L-0.0236 °20.026 °20.0447 °2-1.6087 °20.101 °2--0.0663 °2
S-0.0456 Å °-0.0031 Å °-0.0174 Å °-0.0387 Å °0.036 Å °-0.1131 Å °0.0284 Å °-0.0208 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA27 - 225
2X-RAY DIFFRACTION1allB27 - 225
3X-RAY DIFFRACTION1allC28 - 225
4X-RAY DIFFRACTION1allD28 - 225
5X-RAY DIFFRACTION1allE1 - 8
6X-RAY DIFFRACTION1allF1 - 2
7X-RAY DIFFRACTION1allS1 - 369

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