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- PDB-2wj4: CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUIN... -

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Entry
Database: PDB / ID: 2wj4
TitleCRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) FROM ARTHROBACTER NITROGUAJACOLICUS RU61A ANAEROBICALLY COMPLEXED WITH ITS NATURAL SUBSTRATE 1-H-3-HYDROXY-4-OXOQUINALDINE
Components1H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
KeywordsOXIDOREDUCTASE / ALPHA/BETA HYDROLASE
Function / homology
Function and homology information


3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase / 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / catabolic process
Similarity search - Function
Uteroglobin - #20 / Uteroglobin / : / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Uteroglobin - #20 / Uteroglobin / : / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-HYDROXY-2-METHYLQUINOLIN-4(1H)-ONE / : / S,R MESO-TARTARIC ACID / 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase / 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
Similarity search - Component
Biological speciesARTHROBACTER NITROGUAJACOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å
AuthorsSteiner, R.A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural Basis for Cofactor-Independent Dioxygenation of N-Heteroaromatic Compounds at the {Alpha}/{Beta}-Hydrolase Fold.
Authors: Steiner, R.A. / Janssen, H.J. / Roversi, P. / Oakley, A.J. / Fetzner, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization and Preliminary X-Ray Analysis of 1H-3-Hydroxy-4-Oxoquinaldine 2,4-Dioxygenase from Arthrobacter Nitroguajacolicus Ru61A: A Cofactor-Devoid Dioxygenase of the Alpha/Beta-Hydrolase-Fold Superfamily.
Authors: Steiner, R.A. / Frerichs-Deeken, U. / Fetzner, S.
History
DepositionMay 20, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_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_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
B: 1H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
C: 1H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
D: 1H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,12727
Polymers127,5354
Non-polymers2,59123
Water6,972387
1
A: 1H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,86410
Polymers31,8841
Non-polymers9809
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 1H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4906
Polymers31,8841
Non-polymers6075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: 1H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3405
Polymers31,8841
Non-polymers4564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: 1H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4326
Polymers31,8841
Non-polymers5495
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.810, 167.200, 167.220
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
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 3 / Auth seq-ID: 5 - 274 / Label seq-ID: 5 - 274

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS oper:
IDCodeMatrixVector
1given(0.9993, 0.03621, 0.00986), (-0.03596, 0.99906, -0.02422), (-0.01073, 0.02384, 0.99966)-1.38426, 70.55027, -67.53616
2given(0.99956, -0.02348, 0.01801), (-0.01737, 0.02736, 0.99947), (-0.02396, -0.99935, 0.02694)-10.29444, 23.81576, 124.62343
3given(0.99959, 0.01095, 0.02635), (-0.02626, -0.00781, 0.99962), (0.01115, -0.99991, -0.00752)-14.27918, -40.99587, 58.33015

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
1H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE / 1-H-3-HYDROXY-4-OXOQUINALDINE 2\ / 4-DIOXYGENASE


Mass: 31883.863 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARTHROBACTER NITROGUAJACOLICUS (bacteria)
Strain: RU61A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15/PREP4
References: UniProt: A4V8M9, UniProt: O31266*PLUS, 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase

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Non-polymers , 5 types, 410 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-HQD / 3-HYDROXY-2-METHYLQUINOLIN-4(1H)-ONE


Mass: 175.184 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H9NO2
#5: Chemical
ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 69 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 69 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 69 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 69 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 69 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 69 TO SER
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: 2.36 Å3/Da / Density % sol: 47.45 % / Description: NONE
Crystal growpH: 7
Details: PROTEIN AT 150 MG/ML IN STORAGE BUFFER 1.65M NA/K TARTRATE, 0.1M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9697
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 14, 2008 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9697 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.577
11-H, L, K20.423
ReflectionResolution: 2→39.4 Å / Num. obs: 74241 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 31.99 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.1→38.84 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.645 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20395 3784 5.1 %RANDOM
Rwork0.17602 ---
obs0.17746 70375 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.676 Å2
Baniso -1Baniso -2Baniso -3
1-4.87 Å20 Å20 Å2
2---7.95 Å20 Å2
3---3.07 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8921 0 169 387 9477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0219370
X-RAY DIFFRACTIONr_bond_other_d0.0090.026404
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.93712746
X-RAY DIFFRACTIONr_angle_other_deg1.492.99415444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1551091
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18323.402485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.646151461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6141572
X-RAY DIFFRACTIONr_chiral_restr0.0950.21293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110446
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021994
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_it0.6371.55458
X-RAY DIFFRACTIONr_mcbond_other0.2021.52189
X-RAY DIFFRACTIONr_mcangle_it1.16328815
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0133912
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1524.53930
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1579tight positional0.050.05
2B1579tight positional0.050.05
3C1579tight positional0.050.05
4D1579tight positional0.050.05
1A2189loose positional0.115
2B2189loose positional0.115
3C2189loose positional0.095
4D2189loose positional0.125
1A1579tight thermal0.230.5
2B1579tight thermal0.170.5
3C1579tight thermal0.250.5
4D1579tight thermal0.210.5
1A2189loose thermal0.1810
2B2189loose thermal0.1610
3C2189loose thermal0.1910
4D2189loose thermal0.1710
LS refinement shellResolution: 2.098→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 310 -
Rwork0.207 4833 -
obs--94.21 %

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