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- PDB-2h0v: Crystal structure of a putative quercetin 2,3-dioxygenase (yxag, ... -

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Basic information

Entry
Database: PDB / ID: 2h0v
TitleCrystal structure of a putative quercetin 2,3-dioxygenase (yxag, bsu39980) from bacillus subtilis at 2.60 A resolution
ComponentsQuercetin 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / Double-stranded beta-helix / bicupin / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


quercetin 2,3-dioxygenase / quercetin 2,3-dioxygenase activity / metal ion binding
Similarity search - Function
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
: / L(+)-TARTARIC ACID / Quercetin 2,3-dioxygenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of (2636545) from Bacillus subtilis at 2.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.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 / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 999SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DNA SEQUENCING INDICATES THAT RESIDUE 160 IS ASPARTIC ACID (NOT THREONINE) AND RESIDUE 314 IS GLUTAMIC ACID (NOT LYSINE) IN THE CLONED CONSTRUCT. THE SEQUENCING RESULTS ARE CONSISTENT WITH THE ELECTRON DENSITY AND MASS SPECTROMETRY RESULTS FOR THE EXPRESSED PROTEIN.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,13628
Polymers76,2512
Non-polymers1,88526
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.416, 128.659, 133.889
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUVALVAL4AA4 - 1625 - 163
21LEULEUVALVAL4BB4 - 1625 - 163
32PHEPHEALAALA1AA163 - 173164 - 174
42PHEPHEALAALA1BB163 - 173164 - 174
53LYSLYSARGARG6AA174 - 322175 - 323
63LYSLYSARGARG6BB174 - 322175 - 323
74ILEILELYSLYS5AA323 - 333324 - 334
84ILEILELYSLYS5BB323 - 333324 - 334
95VALVALPROPRO1AA334 - 337335 - 338
105VALVALPROPRO1BB334 - 337335 - 338
116FEFETLATLA4AC - F500 - 503
126FEFETLATLA4BO - R500 - 503

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Quercetin 2,3-dioxygenase / / Quercetinase / Flavonol 2 / 4-dioxygenase


Mass: 38125.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: qdoI / Production host: Escherichia coli (E. coli) / References: UniProt: P42106, quercetin 2,3-dioxygenase

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Non-polymers , 5 types, 338 molecules

#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 5.31 Å3/Da / Density % sol: 76.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 10.0% PEG-3350, 0.4M Ammonium Tartrate, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.019976
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Oct 12, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.019976 Å / Relative weight: 1
ReflectionResolution: 2.6→29.778 Å / Num. obs: 52320 / % possible obs: 99.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 59.22 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRsym value% possible all
2.6-2.674.90.77111869438310.771100
2.67-2.745.40.6731.12017537420.673100
2.74-2.825.50.5161.52011736270.516100
2.82-2.915.50.4351.71957535380.435100
2.91-35.50.3432.21885234250.343100
3-3.115.50.2383.21832033150.238100
3.11-3.225.50.1953.81764632160.195100
3.22-3.365.50.1584.71694730880.158100
3.36-3.515.50.1225.91623729600.122100
3.51-3.685.50.1027.11560728530.10299.9
3.68-3.885.50.0917.81478826910.091100
3.88-4.115.50.0769.21401225590.07699.9
4.11-4.395.50.06111.21312824050.06199.8
4.39-4.755.40.05412.41240422780.05499.7
4.75-5.25.40.052131119720660.05299.6
5.2-5.815.40.05212.91017818880.05299.6
5.81-6.715.30.04614.8890316690.04699.4
6.71-8.225.30.03717.8753514270.03799.1
8.22-11.635.10.0319.9575211290.0398.7
11.63-29.784.60.0272128116130.02792.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1y3tA

Resolution: 2.6→29.78 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 11.787 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.ANOMALOUS DIFFERENCE MAPS INDICATE THE BINDING OF METAL IONS TO THE PROTEIN. X-RAY FLUORESCENCE MEASUREMENTS INDICATE THESE SITES ARE OCCUPIED PREDOMINANTLY BY FERROUS OR FERRIC CATIONS. EACH SUBUNIT CONTAINS TWO BOUND FE ATOMS. 4.ETHYLENE GLYCOL, USED FOR CRYOPROTECTION, WAS MODELED AS A LIGAND TO ONE OF THE FE ATOMS ON EACH SUBUNIT IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. L(+)-TARTRATE ANIONS FROM THE CRYSTALLIZATION WERE MODELED AS LIGANDS TO THE SECOND FE ATOM ON EACH SUBUNIT. 5.ADDITIONAL MOLECULES OF ETHYLENE GLYCOL AND TRIS(HYDROXYMETHYL)AMINOMETHANE WERE MODELED. 6.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2666 5.1 %RANDOM
Rwork0.167 ---
obs0.169 52271 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.565 Å2
Baniso -1Baniso -2Baniso -3
1-5.86 Å20 Å20 Å2
2---3.68 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5206 0 112 312 5630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0215454
X-RAY DIFFRACTIONr_bond_other_d0.0010.024853
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9727358
X-RAY DIFFRACTIONr_angle_other_deg0.808311256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.21723.794253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62315834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4091531
X-RAY DIFFRACTIONr_chiral_restr0.0820.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026077
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021092
X-RAY DIFFRACTIONr_nbd_refined0.1910.2940
X-RAY DIFFRACTIONr_nbd_other0.1850.25067
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22557
X-RAY DIFFRACTIONr_nbtor_other0.0860.23342
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2308
X-RAY DIFFRACTIONr_metal_ion_refined0.1920.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.24
X-RAY DIFFRACTIONr_mcbond_it1.60833430
X-RAY DIFFRACTIONr_mcbond_other0.38231364
X-RAY DIFFRACTIONr_mcangle_it2.60955370
X-RAY DIFFRACTIONr_scbond_it4.54582260
X-RAY DIFFRACTIONr_scangle_it6.309111988
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
191TIGHT POSITIONAL0.050.05
2431MEDIUM POSITIONAL0.270.5
2328LOOSE POSITIONAL0.245
191TIGHT THERMAL0.10.5
2431MEDIUM THERMAL0.722
2328LOOSE THERMAL1.8810
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 211 -
Rwork0.291 3614 -
obs-3825 99.97 %
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)
10.990.4495-0.12172.3737-0.2361.73830.0266-0.08630.17440.28020.03790.2698-0.3119-0.1031-0.0645-0.04140.08060.0387-0.115-0.0138-0.0592-8.37489.5945-28.6032
20.688-0.09080.04322.2175-0.53281.4345-0.04620.0944-0.0573-0.29660.11450.41080.2483-0.2028-0.0684-0.0724-0.0018-0.0635-0.04640.011-0.0359-16.2788-17.2425-43.1058
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 337
2X-RAY DIFFRACTION2B3 - 337

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