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- PDB-6d0g: 1.78 Angstrom Resolution Crystal Structure of Quercetin 2,3-dioxy... -

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Basic information

Entry
Database: PDB / ID: 6d0g
Title1.78 Angstrom Resolution Crystal Structure of Quercetin 2,3-dioxygenase from Acinetobacter baumannii
ComponentsPirin family protein
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Quercetin 2 / 3-dioxygenase
Function / homology
Function and homology information


quercetin 2,3-dioxygenase / quercetin 2,3-dioxygenase activity / metal ion binding
Similarity search - Function
Pirin, C-terminal domain / Pirin C-terminal cupin domain / Pirin, N-terminal domain / Pirin / Pirin / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
BROMIDE ION / : / Cytoplasmic protein
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsMinasov, G. / Shuvalova, L. / Brunzelle, J.S. / Dubrovska, I. / Kiryukhina, O. / Endres, M. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.78 Angstrom Resolution Crystal Structure of Quercetin 2,3-dioxygenase from Acinetobacter baumannii.
Authors: Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Dubrovska, I. / Kiryukhina, O. / Endres, M. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A.
History
DepositionApr 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pirin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3744
Polymers36,1591
Non-polymers2153
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-7 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.883, 73.616, 202.741
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-579-

HOH

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Components

#1: Protein Pirin family protein / Quercetin 2 / 3-dioxygenase


Mass: 36159.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: yhhW_2, yhhW_1, A388_00159, A7A65_05705, A7M90_08420, A7N09_08935, AZE33_00735, B4R90_09220, B9X91_00175, BGC29_04645, CAS83_08120, CBE85_14535, CEJ63_12860, CHQ89_16690, CPI82_15400, CV954_18565, LV38_01393
Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: V5VHS3, quercetin 2,3-dioxygenase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 8.0 mg/mL protein in 0.01 M Tris, pH 8.3, screen: PACT (F2) (0.2 M sodium bromide, 0.1 M Bis-Tris propane, pH 6.5, 20% w/v PEG3350)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 6, 2018 / Details: C(111)
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.78→30 Å / Num. obs: 29760 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 13.3 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.026 / Rrim(I) all: 0.098 / Rsym value: 0.095 / Χ2: 1.382 / Net I/σ(I): 29.3
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1272 / CC1/2: 0.773 / Rpim(I) all: 0.223 / Rrim(I) all: 0.79 / Rsym value: 0.755 / Χ2: 0.998 / % possible all: 85.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.78→29.78 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.298 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21009 1472 5 %RANDOM
Rwork0.17438 ---
obs0.17629 28236 97.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.645 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å20 Å2
2--0.53 Å20 Å2
3---0.84 Å2
Refinement stepCycle: 1 / Resolution: 1.78→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 3 235 2595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192516
X-RAY DIFFRACTIONr_bond_other_d0.0010.022310
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9663442
X-RAY DIFFRACTIONr_angle_other_deg0.84735384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6585320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.74424.655116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.15315377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.2491513
X-RAY DIFFRACTIONr_chiral_restr0.090.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.0212852
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02493
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9961.7081250
X-RAY DIFFRACTIONr_mcbond_other0.9881.7071249
X-RAY DIFFRACTIONr_mcangle_it1.4612.5591580
X-RAY DIFFRACTIONr_mcangle_other1.4612.561581
X-RAY DIFFRACTIONr_scbond_it1.9191.961266
X-RAY DIFFRACTIONr_scbond_other1.9191.9611266
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7792.8361862
X-RAY DIFFRACTIONr_long_range_B_refined5.25121.5422667
X-RAY DIFFRACTIONr_long_range_B_other5.15620.8312610
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.781→1.827 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 73 -
Rwork0.234 1867 -
obs--87.15 %
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)
15.0184-2.90993.60424.8745-3.9886.55640.12410.0314-0.0961-0.1427-0.0677-0.26080.14850.3267-0.05640.00670.01340.0070.07620.00420.0513.449-0.198226.0692
21.75920.11790.37921.2129-0.18370.98080.0241-0.2394-0.02750.0390.02370.0088-0.0119-0.0161-0.04780.066-0.00560.00050.0550.01550.0118-2.92952.516228.1304
33.08120.5455-0.15722.62790.90082.2710.1368-0.6968-0.15030.27290.0375-0.26390.04420.361-0.17430.12080.0054-0.07020.30560.03990.077311.7848-1.155138.1104
41.64830.181-0.15722.6148-0.83993.24120.01290.1752-0.2228-0.4726-0.0254-0.02070.36070.19640.01250.17360.01-0.01650.0438-0.01070.047-3.4075-7.343310.4403
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 41
2X-RAY DIFFRACTION2A42 - 198
3X-RAY DIFFRACTION3A199 - 258
4X-RAY DIFFRACTION4A259 - 315

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