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- PDB-3zph: Bacterial chalcone isomerase in closed conformation from Eubacter... -

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Basic information

Entry
Database: PDB / ID: 3zph
TitleBacterial chalcone isomerase in closed conformation from Eubacterium ramulus at 2.8 A resolution
ComponentsCHALCONE ISOMERASE
KeywordsISOMERASE / FLAVONOID DEGRADATION
Function / homologyChalcone isomerase, N-terminal / Chalcone isomerase N-terminal domain / Chalcone_N domain-containing protein
Function and homology information
Biological speciesEUBACTERIUM RAMULUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsThomsen, M. / Palm, G.J. / Hinrichs, W.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Enzymatic conversion of flavonoids using bacterial chalcone isomerase and enoate reductase.
Authors: Gall, M. / Thomsen, M. / Peters, C. / Pavlidis, I.V. / Jonczyk, P. / Grunert, P.P. / Beutel, S. / Scheper, T. / Gross, E. / Backes, M. / Geissler, T. / Ley, J.P. / Hilmer, J.M. / Krammer, G. ...Authors: Gall, M. / Thomsen, M. / Peters, C. / Pavlidis, I.V. / Jonczyk, P. / Grunert, P.P. / Beutel, S. / Scheper, T. / Gross, E. / Backes, M. / Geissler, T. / Ley, J.P. / Hilmer, J.M. / Krammer, G. / Palm, G.J. / Hinrichs, W. / Bornscheuer, U.T.
#1: Journal: Arch.Microbiol. / Year: 2004
Title: First Bacterial Chalcone Isomerase Isolated from Eubacterium Ramulus.
Authors: Herles, C. / Braune, A. / Blaut, M.
History
DepositionFeb 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ASTM / _citation.journal_id_CSD ..._citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHALCONE ISOMERASE
B: CHALCONE ISOMERASE
C: CHALCONE ISOMERASE
D: CHALCONE ISOMERASE
E: CHALCONE ISOMERASE
F: CHALCONE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,04315
Polymers194,4406
Non-polymers6029
Water19,1141061
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29870 Å2
ΔGint-171.6 kcal/mol
Surface area52050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.730, 203.120, 206.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-2031-

HOH

21B-2091-

HOH

31E-2072-

HOH

41F-2017-

HOH

51F-2139-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9886, 0.09846, -0.11391), (0.08525, -0.25759, -0.96249), (-0.12411, -0.96122, 0.24626)31.87341, 46.79527, 39.07657
2given(0.07543, 0.10299, 0.99182), (0.99674, 0.02092, -0.07798), (-0.02878, 0.99446, -0.10107)-9.6819, 6.66119, 3.93938
3given(0.07981, 0.99628, -0.03249), (0.1033, 0.02416, 0.99436), (0.99144, -0.08272, -0.10099)-5.83395, -3.20805, 10.60501
4given(0.02627, -0.21608, -0.97602), (-0.22767, -0.95199, 0.20463), (-0.97338, 0.21683, -0.0742)41.78625, 40.27099, 34.80331
5given(-0.18738, -0.97206, 0.14138), (-0.97194, 0.16265, -0.16992), (0.14218, -0.16926, -0.97526)36.26998, 36.82818, 45.39044

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Components

#1: Protein
CHALCONE ISOMERASE


Mass: 32406.736 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EUBACTERIUM RAMULUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: U2Q8X2*PLUS, chalcone isomerase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1061 / 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: 4.9 Å3/Da / Density % sol: 75 %
Description: SELENOMET STRUCTURE UNDER REFINEMENT. TO BE PUBLISHED
Crystal growpH: 7.5
Details: 0.1 M HEPES PH 7.5, 0.2 M NACL, 1.8 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Oct 15, 2012 / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20.1 Å / Num. obs: 91147 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 5.4
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0027refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C9S

4c9s


Resolution: 2.8→20.09 Å / Cor.coef. Fo:Fc: 0.86 / Cor.coef. Fo:Fc free: 0.819 / SU B: 27.522 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.484 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.29661 4539 5 %RANDOM
Rwork0.24794 ---
obs0.25038 86192 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.25 Å2
Baniso -1Baniso -2Baniso -3
1--2.13 Å20 Å20 Å2
2--0.33 Å20 Å2
3---1.8 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12907 0 34 1061 14002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213383
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212327
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.94318204
X-RAY DIFFRACTIONr_angle_other_deg0.784328447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9651573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38923.982653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.387152152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.341567
X-RAY DIFFRACTIONr_chiral_restr0.0790.21848
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02115045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023204
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 368 -
Rwork0.411 6370 -
obs--99.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.47920.08890.16470.3347-0.04631.04330.0028-0.06070.0330.0717-0.01620.0553-0.0584-0.04570.01350.490.04740.00690.020.00920.04339.03334.38446.399
20.28420.14340.00530.9144-0.22360.3559-0.00850.0525-0.0896-0.11180.0261-0.02070.1610.0549-0.01760.57130.03010.05920.10070.00250.042321.167-5.66915.186
30.4904-0.06320.04630.7208-0.22630.4913-0.00760.05820.1143-0.0861-0.0316-0.0805-0.06310.1070.03930.45810.00080.04690.06460.02590.038327.78944.71412.165
40.98770.03080.05110.70970.02060.4223-0.0354-0.0646-0.04140.02990.0366-0.10550.01440.2011-0.00120.46120.04190.01320.16910.03820.041140.54412.84333.217
50.8289-0.17540.13780.41140.22480.4778-0.01470.0168-0.03110.0024-0.01090.14420.0578-0.11150.02570.4693-0.02430.01020.05570.03790.0925-10.79415.22629.852
60.93050.1925-0.03460.76340.11791.1478-0.0350.18510.0455-0.18080.00790.10650.0211-0.08270.0270.55580.0349-0.01950.14230.03860.02737.68125.809-4.401
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 282
2X-RAY DIFFRACTION2B1 - 282
3X-RAY DIFFRACTION3C1 - 282
4X-RAY DIFFRACTION4D1 - 282
5X-RAY DIFFRACTION5E1 - 282
6X-RAY DIFFRACTION6F1 - 282

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