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- PDB-5fli: enzyme-substrate complex of Ni-quercetinase -

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Basic information

Entry
Database: PDB / ID: 5fli
Titleenzyme-substrate complex of Ni-quercetinase
ComponentsQUERCETINASE QUED
KeywordsOXIDOREDUCTASE / DIOXYGENASE / NICKEL / QUERCETIN / STREPTOMYCES / NI-QUUERCETINASE
Function / homology
Function and homology information


: / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / Quercetinase QueD
Similarity search - Component
Biological speciesSTREPTOMYCES SP. FLA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJeoung, J.-H. / Nianios, D. / Fetzner, S. / Dobbek, H.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2016
Title: Quercetin 2,4-Dioxygenase Activates Dioxygen in a Side-On O2-Ni Complex.
Authors: Jeoung, J.H. / Nianios, D. / Fetzner, S. / Dobbek, H.
History
DepositionOct 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3May 24, 2017Group: Database references
Revision 1.4Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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 1.5Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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 / _struct_conn.ptnr2_label_seq_id / _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: QUERCETINASE QUED
B: QUERCETINASE QUED
C: QUERCETINASE QUED
D: QUERCETINASE QUED
E: QUERCETINASE QUED
F: QUERCETINASE QUED
G: QUERCETINASE QUED
H: QUERCETINASE QUED
I: QUERCETINASE QUED
J: QUERCETINASE QUED
K: QUERCETINASE QUED
L: QUERCETINASE QUED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,15235
Polymers253,12312
Non-polymers4,02923
Water16,141896
1
K: QUERCETINASE QUED
L: QUERCETINASE QUED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9096
Polymers42,1872
Non-polymers7224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-75.1 kcal/mol
Surface area15510 Å2
MethodPISA
2
E: QUERCETINASE QUED
F: QUERCETINASE QUED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9096
Polymers42,1872
Non-polymers7224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-76.4 kcal/mol
Surface area15700 Å2
MethodPISA
3
G: QUERCETINASE QUED
H: QUERCETINASE QUED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9096
Polymers42,1872
Non-polymers7224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-77.7 kcal/mol
Surface area15840 Å2
MethodPISA
4
I: QUERCETINASE QUED
J: QUERCETINASE QUED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6075
Polymers42,1872
Non-polymers4203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-66.3 kcal/mol
Surface area15780 Å2
MethodPISA
5
B: QUERCETINASE QUED
C: QUERCETINASE QUED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9096
Polymers42,1872
Non-polymers7224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-75.2 kcal/mol
Surface area15720 Å2
MethodPISA
6
A: QUERCETINASE QUED
D: QUERCETINASE QUED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9096
Polymers42,1872
Non-polymers7224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-75.9 kcal/mol
Surface area15840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.396, 113.752, 105.003
Angle α, β, γ (deg.)90.00, 96.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
QUERCETINASE QUED / NI-QUERECETINASE


Mass: 21093.562 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES SP. FLA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A2VA43, quercetin 2,3-dioxygenase
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C15H10O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 896 / 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: 2.4 Å3/Da / Density % sol: 48.7 % / Description: NONE
Crystal growpH: 8
Details: 0.1 M CACL2, 0.1 M TRIS-HCL PH 8.0, 10 - 13% PEG6000 AND 5% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorDetector: CCD
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.15→47.5 Å / Num. obs: 128091 / % possible obs: 99.7 % / Observed criterion σ(I): 1.2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.6
Reflection shellResolution: 2.15→2.23 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FLH

5flh


Resolution: 2.15→47.505 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 27.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 6405 5 %
Rwork0.1954 --
obs0.1973 128091 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→47.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17664 0 254 896 18814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00718598
X-RAY DIFFRACTIONf_angle_d1.1525314
X-RAY DIFFRACTIONf_dihedral_angle_d15.3676700
X-RAY DIFFRACTIONf_chiral_restr0.0852484
X-RAY DIFFRACTIONf_plane_restr0.0053400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1483-2.17270.38741930.3383677X-RAY DIFFRACTION91
2.1727-2.19830.4142140.34074056X-RAY DIFFRACTION100
2.1983-2.22510.35342120.33414035X-RAY DIFFRACTION100
2.2251-2.25330.37182150.3224098X-RAY DIFFRACTION100
2.2533-2.28290.32642120.30764022X-RAY DIFFRACTION100
2.2829-2.31420.3242150.294082X-RAY DIFFRACTION100
2.3142-2.34730.33282120.28554034X-RAY DIFFRACTION100
2.3473-2.38230.29922150.27174091X-RAY DIFFRACTION100
2.3823-2.41950.32612120.25284041X-RAY DIFFRACTION99
2.4195-2.45920.30292140.25034054X-RAY DIFFRACTION100
2.4592-2.50160.33182140.25414062X-RAY DIFFRACTION100
2.5016-2.54710.31612120.25134036X-RAY DIFFRACTION100
2.5471-2.59610.28752130.24334044X-RAY DIFFRACTION100
2.5961-2.64910.29512140.23774063X-RAY DIFFRACTION100
2.6491-2.70670.28052150.22554084X-RAY DIFFRACTION100
2.7067-2.76960.27362130.21974061X-RAY DIFFRACTION100
2.7696-2.83890.26752140.22134056X-RAY DIFFRACTION100
2.8389-2.91560.30142150.21844084X-RAY DIFFRACTION100
2.9156-3.00140.25242130.20514047X-RAY DIFFRACTION100
3.0014-3.09820.24582150.19774082X-RAY DIFFRACTION100
3.0982-3.2090.23172130.19194051X-RAY DIFFRACTION100
3.209-3.33740.22292150.18474082X-RAY DIFFRACTION100
3.3374-3.48930.23222140.18484073X-RAY DIFFRACTION99
3.4893-3.67320.20362150.17494076X-RAY DIFFRACTION100
3.6732-3.90320.17732150.16574096X-RAY DIFFRACTION100
3.9032-4.20440.21352150.1624074X-RAY DIFFRACTION100
4.2044-4.62720.16562150.14044087X-RAY DIFFRACTION99
4.6272-5.2960.18162150.15254089X-RAY DIFFRACTION99
5.296-6.66940.20292160.17534106X-RAY DIFFRACTION100
6.6694-47.51620.1852200.17264163X-RAY DIFFRACTION99

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