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- PDB-6adu: Crystal structure of an enzyme in complex with ligand C -

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Basic information

Entry
Database: PDB / ID: 6adu
TitleCrystal structure of an enzyme in complex with ligand C
Componentsacyclase
KeywordsTRANSFERASE / prenyltransferase
Function / homologyHpiC1 cyclase / metal ion binding / (3~{Z})-3-(1-methylpyrrolidin-2-ylidene)indole / 12-epi-hapalindole U synthase / 12-epi-hapalindole U synthase
Function and homology information
Biological speciesFischerella ambigua UTEX 1903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsTan, X.K. / 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
DepositionAug 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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: acyclase
B: acyclase
C: acyclase
D: acyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,48020
Polymers98,8234
Non-polymers1,65716
Water11,944663
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-73 kcal/mol
Surface area31550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.773, 256.546, 36.043
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
acyclase


Mass: 24705.799 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella ambigua UTEX 1903 (bacteria)
Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1P8VSI6, UniProt: V5TER4*PLUS

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Non-polymers , 5 types, 679 molecules

#2: Chemical
ChemComp-9UL / (3~{Z})-3-(1-methylpyrrolidin-2-ylidene)indole


Mass: 198.264 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H14N2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 663 / 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: 40.09 % / Mosaicity: 2.036 °
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: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 26, 2018 / Details: LN2 cooled Si(111) double crystal monochromator
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 58487 / % possible obs: 97.6 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.024 / Rrim(I) all: 0.091 / Χ2: 1.111 / Net I/σ(I): 6.5 / Num. measured all: 862118
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-2.0215.40.50958800.9630.1330.5270.65699.9
2.02-2.116.30.40958900.980.1040.4230.73299.8
2.1-2.216.50.32958530.9860.0830.340.78299.8
2.2-2.3116.30.25958900.9910.0660.2680.83699.7
2.31-2.4616.30.20159020.9940.0520.2080.89399.5
2.46-2.6515.40.14858910.9960.0390.1531.0499.3
2.65-2.9114.70.1158830.9960.030.1141.19398.3
2.91-3.3313.20.07957660.9970.0220.0831.53695.8
3.33-4.211.30.06155380.9970.0180.0641.98891
4.2-2511.90.0559940.9980.0150.0522.12993.6

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Processing

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

5yvk


Resolution: 1.96→24.67 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.485 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.175 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24675 2856 4.9 %RANDOM
Rwork0.18425 ---
obs0.18738 55525 96.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.148 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å20 Å2-0 Å2
2---2.65 Å20 Å2
3---0.7 Å2
Refinement stepCycle: 1 / Resolution: 1.96→24.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6126 0 107 663 6896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0146401
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175650
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.6848747
X-RAY DIFFRACTIONr_angle_other_deg0.8751.65713208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8025795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74724.177316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19315945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7391522
X-RAY DIFFRACTIONr_chiral_restr0.1220.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027249
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021225
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_it2.6223.3583181
X-RAY DIFFRACTIONr_mcbond_other2.6213.3573180
X-RAY DIFFRACTIONr_mcangle_it3.3965.0173969
X-RAY DIFFRACTIONr_mcangle_other3.3975.0173970
X-RAY DIFFRACTIONr_scbond_it3.2333.6983220
X-RAY DIFFRACTIONr_scbond_other3.2323.6983221
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.715.4254777
X-RAY DIFFRACTIONr_long_range_B_refined6.20740.2327087
X-RAY DIFFRACTIONr_long_range_B_other6.11639.6766929
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.956→2.007 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 196 -
Rwork0.223 3773 -
obs--90.06 %

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