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- PDB-1h1i: CRYSTAL STRUCTURE OF QUERCETIN 2,3-DIOXYGENASE ANAEROBICALLY COMP... -

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Entry
Database: PDB / ID: 1h1i
TitleCRYSTAL STRUCTURE OF QUERCETIN 2,3-DIOXYGENASE ANAEROBICALLY COMPLEXED WITH THE SUBSTRATE QUERCETN
ComponentsQUERCETIN 2,3-DIOXYGENASE
KeywordsOXIDOREDUCTASE / DIOXYGENASE / FLAVONOL
Function / homology
Function and homology information


quercetin 2,3-dioxygenase / quercetin 2,3-dioxygenase activity / metal ion binding
Similarity search - Function
: / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / Quercetin 2,3-dioxygenase
Similarity search - Component
Biological speciesASPERGILLUS JAPONICUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.75 Å
AuthorsSteiner, R.A. / Dijkstra, B.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Anaerobic Enzyme.Substrate Structures Provide Insight Into the Reaction Mechanism of the Copper- Dependent Quercetin 2,3-Dioxygenase.
Authors: Steiner, R.A. / Kalk, K.H. / Dijkstra, B.W.
History
DepositionJul 15, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: QUERCETIN 2,3-DIOXYGENASE
B: QUERCETIN 2,3-DIOXYGENASE
C: QUERCETIN 2,3-DIOXYGENASE
D: QUERCETIN 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,13933
Polymers151,8334
Non-polymers6,30629
Water27,7251539
1
A: QUERCETIN 2,3-DIOXYGENASE
C: QUERCETIN 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,28217
Polymers75,9162
Non-polymers3,36515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: QUERCETIN 2,3-DIOXYGENASE
D: QUERCETIN 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,85716
Polymers75,9162
Non-polymers2,94114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)109.298, 55.745, 124.163
Angle α, β, γ (deg.)90.00, 98.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
QUERCETIN 2,3-DIOXYGENASE


Mass: 37958.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS JAPONICUS (mold) / Production host: ASPERGILLUS AWAMORI (mold) / References: UniProt: Q7SIC2, quercetin 2,3-dioxygenase

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Sugars , 2 types, 17 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 1551 molecules

#4: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#5: Chemical
ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H10O7
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1539 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.5 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.2
Details: HANGING DROP, 21-23% PEG 8000, 200 MM AMMONIUM SULFATE, 100 MM CITRATE BUFFER, PH 5.2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
250 mMMES1droppH6.0
321-23 %(w/v)PEG80001reservoir
4200 mMammonium sulfate1reservoir
5100 mMsodium citrate1reservoirpH5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.935
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.935 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 148198 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 28.2
Reflection shellResolution: 1.75→1.76 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.6 / % possible all: 69.4
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 99.4 %
Reflection shell
*PLUS
% possible obs: 69.4 % / Rmerge(I) obs: 0.25

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.75→49.39 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.963 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.183 7473 5 %RANDOM
Rwork0.148 ---
obs0.15 141342 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20.34 Å2
2--1.35 Å20 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 1.75→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10580 0 404 1539 12523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02111376
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.95715622
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40651368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1170.21737
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028840
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.25214
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.21277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.2202
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.291
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8141.56844
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.392211121
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.39734532
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6964.54501
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: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.281 526
Rwork0.234 10220
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)
10.50250.0233-0.03180.25150.19321.0918-0.0066-0.1559-0.07750.0982-0.0621-0.06350.04320.08320.06880.0524-0.0194-0.01660.06520.03650.091367.545413.84671.374
20.73330.0427-0.12580.9358-0.03731.34350.003-0.0435-0.0129-0.0417-0.0379-0.00150.0277-0.05970.0350.0192-0.0106-0.01160.0060.00280.064757.745915.786759.9936
30.9350.0354-0.14360.393-0.14420.87210.0083-0.12020.09820.1785-0.00770.0708-0.13680.0324-0.00060.1102-0.00420.00850.12870.01740.084486.289826.1299.5089
40.66570.1498-0.03870.82330.14831.6807-0.011-0.0770.00660.12390.02440.00610.03360.1639-0.01340.05340.0204-0.00520.11750.03760.071492.564815.1790.9092
50.91380.0515-0.24210.1071-0.17281.2696-0.03450.1164-0.1241-0.1912-0.052-0.03670.17380.15870.08650.13810.02660.03740.0740.01680.102875.829210.716537.3829
60.8159-0.041-0.24591.1006-0.09641.61430.01330.0037-0.0413-0.1063-0.0665-0.16630.07250.31560.05320.0440.02260.02330.1340.05720.122285.650714.439848.2375
70.18720.07470.11790.7899-0.30330.9003-0.0147-0.07840.03650.12150.01590.0208-0.1404-0.0186-0.00120.0828-0.0023-0.01730.1098-0.03890.086121.9614-0.914425.4223
80.6414-0.2243-0.04081.035-0.0711.48290.0079-0.02140.06370.03270.007-0.1198-0.19260.1403-0.01480.0848-0.0535-0.02890.1012-0.03870.109432.52385.993117.0052
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 154
2X-RAY DIFFRACTION1A1357
3X-RAY DIFFRACTION1A1358
4X-RAY DIFFRACTION2A159 - 350
5X-RAY DIFFRACTION3B3 - 156
6X-RAY DIFFRACTION3B1355
7X-RAY DIFFRACTION3B1356
8X-RAY DIFFRACTION4B159 - 350
9X-RAY DIFFRACTION5C3 - 153
10X-RAY DIFFRACTION5C1357
11X-RAY DIFFRACTION5C1358
12X-RAY DIFFRACTION6C159 - 350
13X-RAY DIFFRACTION7D4 - 154
14X-RAY DIFFRACTION7D1356
15X-RAY DIFFRACTION7D1357
16X-RAY DIFFRACTION8D159 - 350
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.1501 / Rfactor Rfree: 0.189 / Rfactor Rwork: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.23

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