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- PDB-1gqh: Quercetin 2,3-dioxygenase in complex with the inhibitor kojic acid -

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Basic information

Entry
Database: PDB / ID: 1gqh
TitleQuercetin 2,3-dioxygenase in complex with the inhibitor kojic acid
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 / 5-HYDROXY-2-(HYDROXYMETHYL)-4H-PYRAN-4-ONE / Quercetin 2,3-dioxygenase
Similarity search - Component
Biological speciesASPERGILLUS JAPONICUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.15 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / 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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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

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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)157,81828
Polymers151,8334
Non-polymers5,98524
Water18,3571019
1
B: QUERCETIN 2,3-DIOXYGENASE
D: QUERCETIN 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,60713
Polymers75,9162
Non-polymers2,69011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-2.35 kcal/mol
Surface area23970 Å2
MethodPISA
2
A: QUERCETIN 2,3-DIOXYGENASE
C: QUERCETIN 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,21115
Polymers75,9162
Non-polymers3,29513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint2.77 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.640, 55.396, 124.425
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 , 4 types, 16 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_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 alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
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, 1027 molecules

#5: Chemical
ChemComp-KOJ / 5-HYDROXY-2-(HYDROXYMETHYL)-4H-PYRAN-4-ONE


Mass: 142.109 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O4
#6: Chemical
ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 1019 / 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: 2.32 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: ESRF / Beamline: BM14 / Wavelength: 1.033
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1999 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.15→38.07 Å / Num. obs: 72101 / % possible obs: 89.2 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 3 / % possible all: 86.5
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 150878 / Rmerge(I) obs: 0.13
Reflection shell
*PLUS
% possible obs: 86.5 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.15→49.39 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.751 / SU ML: 0.151 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3587 5 %RANDOM
Rwork0.178 ---
obs0.181 68127 89.2 %-
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: 2.15→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10336 0 379 1019 11734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02111065
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.3591.95515189
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_restr0.0880.21707
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028584
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.35357
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.51698
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.14608
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.3194
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.565
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4841.56654
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.885210785
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.66234411
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6284.54404
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: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.284 239
Rwork0.205 4883
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)
10.75580.03880.01690.62980.34420.88580.0201-0.0778-0.03070.1202-0.0578-0.09960.05140.04360.03770.0479-0.0076-0.02350.06650.01940.066967.353413.891871.2971
20.6535-0.004-0.09831.030.21751.0531-0.0033-0.0245-0.017-0.0325-0.00210.038-0.0081-0.12730.00540.0073-0.0062-0.01830.0455-0.00390.055357.061415.860459.7488
30.6583-0.147-0.20680.4839-0.08050.4812-0.0094-0.14250.09120.14090.01120.0681-0.07290.0465-0.00170.0904-0.01040.00460.1288-0.00880.08785.725225.75419.2635
40.45910.0862-0.02580.87220.17961.2033-0.029-0.094-0.02810.10390.0264-0.00840.09160.11880.00250.0410.0174-0.01170.1010.01880.080492.108114.01210.1034
50.72190.1089-0.24350.5240.01430.9333-0.01930.1202-0.1091-0.23870.0015-0.02170.12240.03290.01780.1150.00860.02120.08930.00040.085475.209110.748537.2685
60.80390.1613-0.21060.9557-0.24431.17450.0168-0.0163-0.0216-0.0896-0.0327-0.21310.01280.22170.01590.04840.01640.00740.10110.01440.119486.049215.317649.0105
70.1690.24080.06240.6164-0.32670.79360.0022-0.07580.05910.15610.00670.0664-0.121-0.0266-0.00890.1017-0.0034-0.01440.0813-0.01850.088521.9608-0.896525.661
80.7009-0.07780.0711.0276-0.17761.37680.0499-0.02240.07160.0564-0.0266-0.1454-0.16870.1752-0.02330.0775-0.0401-0.02390.0884-0.01250.100833.76586.228116.4438
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 154
2X-RAY DIFFRACTION1A1352
3X-RAY DIFFRACTION1A1351
4X-RAY DIFFRACTION2A163 - 350
5X-RAY DIFFRACTION3B3 - 153
6X-RAY DIFFRACTION3B1352
7X-RAY DIFFRACTION3B1351
8X-RAY DIFFRACTION4B168 - 350
9X-RAY DIFFRACTION5C3 - 154
10X-RAY DIFFRACTION5C1352
11X-RAY DIFFRACTION5C1351
12X-RAY DIFFRACTION6C170 - 350
13X-RAY DIFFRACTION7D4 - 153
14X-RAY DIFFRACTION7D1352
15X-RAY DIFFRACTION7D1351
16X-RAY DIFFRACTION8D170 - 350
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4

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