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- PDB-1gqg: Quercetin 2,3-dioxygenase in complex with the inhibitor diethyldi... -

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Basic information

Entry
Database: PDB / ID: 1gqg
TitleQuercetin 2,3-dioxygenase in complex with the inhibitor diethyldithiocarbamate
ComponentsQUERCETIN 2,3-DIOXYGENASE
KeywordsOXIDOREDUCTASE / DIOXYGENASE
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 / DIETHYLCARBAMODITHIOIC ACID / Quercetin 2,3-dioxygenase
Similarity search - Component
Biological speciesASPERGILLUS JAPONICUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 Å
AuthorsSteiner, R.A. / Dijkstra, B.W.
CitationJournal: Biochemistry / Year: 2002
Title: Functional Analysis of the Copper-Dependent Quercetin 2,3-Dioxygenase.1.Ligand-Induced Coordination Changes Probed by X-Ray Crystallography: Inhibition, Ordering Effect and Mechanistic Insights
Authors: Steiner, R.A. / Kooter, I.M. / Dijkstra, B.W.
History
DepositionNov 23, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 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 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _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)157,15728
Polymers151,8334
Non-polymers5,32424
Water26,0141444
1
A: QUERCETIN 2,3-DIOXYGENASE
C: QUERCETIN 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,84214
Polymers75,9162
Non-polymers2,92612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-13.6 kcal/mol
Surface area24370 Å2
MethodPISA
2
B: QUERCETIN 2,3-DIOXYGENASE
D: QUERCETIN 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,31514
Polymers75,9162
Non-polymers2,39912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-20.8 kcal/mol
Surface area24050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.939, 55.646, 123.863
Angle α, β, γ (deg.)90.00, 98.26, 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*PLUS, quercetin 2,3-dioxygenase

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Sugars , 3 types, 16 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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.: 1
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
#6: 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.: 13
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 , 3 types, 1452 molecules

#4: Chemical
ChemComp-DCD / DIETHYLCARBAMODITHIOIC ACID


Mass: 149.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H11NS2
#5: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1444 / 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, 10 MM NA DIETHYLDITHIOCARBAMATE
Crystal grow
*PLUS
pH: 6 / 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
610 mMDDC1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.845
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1999 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.845 Å / Relative weight: 1
ReflectionResolution: 1.7→19.92 Å / Num. obs: 148198 / % possible obs: 91.3 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.1
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 4.5 / % possible all: 69.4
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 91.1 % / Num. measured all: 637059
Reflection shell
*PLUS
% possible obs: 69.4 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.7→19.92 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.009 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.183 7426 5 %RANDOM
Rwork0.161 ---
obs0.162 140366 91.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 1.7→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10321 0 324 1444 12089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02111024
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.3051.94815137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
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_restr0.0890.21703
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028564
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.35124
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.51795
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.3180
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.569
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5211.56655
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.942210804
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.72934369
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7994.54330
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: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.259 427
Rwork0.198 7945
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)
10.51310.1189-0.12640.54050.04771.1011-0.0143-0.1286-0.08480.1125-0.0501-0.06030.03320.0970.06440.0436-0.0169-0.02940.08320.02920.074467.491614.042271.3187
20.6557-0.0125-0.07961.0599-0.04731.2274-0.004-0.0223-0.0013-0.0764-0.00080.06110.0151-0.10810.00480.0113-0.0117-0.020.03190.00010.056856.861816.626358.7575
30.3952-0.1041-0.16210.31130.050.55990.0356-0.150.10230.1843-0.07470.0622-0.12390.00430.03910.1202-0.02980.0070.1305-0.00110.101886.448525.86329.6403
40.64160.07780.031.11670.19341.6180.0223-0.0616-0.00060.117-0.0315-0.03780.07020.15420.00920.05330.0051-0.00550.08660.02690.0792.498414.0750.4629
51.02360.1503-0.30520.3-0.39571.2397-0.06750.1447-0.18-0.2485-0.0281-0.05420.17790.150.09560.14430.00730.03610.1051-0.00440.110375.772510.876437.5062
60.90750.0601-0.23991.1173-0.14221.5172-0.0184-0.0155-0.0878-0.0929-0.0406-0.19760.06310.35980.0590.04090.00470.02010.17790.04950.13386.303715.143248.7778
70.1455-0.02230.07960.9489-0.27031.2131-0.0014-0.08050.0320.1457-0.02220.032-0.1901-0.0240.02360.1055-0.0056-0.02050.0786-0.02510.083321.9364-0.929325.2359
80.6522-0.17860.01531.071-0.07711.34630.0220.00790.09190.0536-0.0403-0.2051-0.23320.20220.01840.1131-0.0601-0.03180.1038-0.00040.127333.75726.345215.8767
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 154
2X-RAY DIFFRACTION1A1352
3X-RAY DIFFRACTION1A1351
4X-RAY DIFFRACTION2A170 - 350
5X-RAY DIFFRACTION3B4 - 153
6X-RAY DIFFRACTION3B1352
7X-RAY DIFFRACTION3B1351
8X-RAY DIFFRACTION4B167 - 350
9X-RAY DIFFRACTION5C3 - 154
10X-RAY DIFFRACTION5C1352
11X-RAY DIFFRACTION5C1351
12X-RAY DIFFRACTION6C166 - 350
13X-RAY DIFFRACTION7D4 - 155
14X-RAY DIFFRACTION7D1352
15X-RAY DIFFRACTION7D1351
16X-RAY DIFFRACTION8D170 - 350
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.184 / Rfactor Rwork: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.3

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