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- PDB-2wj3: CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUIN... -

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Basic information

Entry
Database: PDB / ID: 2wj3
TitleCRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) FROM ARTHROBACTER NITROGUAJACOLICUS RU61A
Components1-H-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 / :
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 / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
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 / MOLECULAR REPLACEMENT / Resolution: 2.09 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)128,92014
Polymers127,5354
Non-polymers1,38510
Water5,026279
1
A: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2764
Polymers31,8841
Non-polymers3923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2764
Polymers31,8841
Non-polymers3923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1843
Polymers31,8841
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1843
Polymers31,8841
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.170, 167.860, 168.030
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A5 - 274
2113B5 - 274
3113C5 - 274
4113D5 - 274

NCS oper:
IDCodeMatrixVector
1given(0.99909, 0.03136, 0.02895), (-0.03048, 0.99907, -0.03036), (-0.02987, 0.02945, 0.99912)-3.56611, 71.48642, -68.47247
2given(0.99941, -0.03329, 0.00796), (-0.007, 0.02877, 0.99956), (-0.03351, -0.99903, 0.02852)-9.02991, 23.85075, 124.84
3given(0.99949, -0.00341, 0.03165), (-0.03162, 0.00668, 0.99948), (-0.00362, -0.99997, 0.00657)-14.87078, -41.87589, 56.86059

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Components

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
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
Nonpolymer detailsGLYCEROL (GOL): PRESENT IN THE SOLUTION FOR CRYOPROTECTION D(-)-TARTARIC ACID (TAR): PRESENT IN THE ...GLYCEROL (GOL): PRESENT IN THE SOLUTION FOR CRYOPROTECTION D(-)-TARTARIC ACID (TAR): PRESENT IN THE CRYSTALLIZATION CONDITION

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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: 2.44 Å3/Da / Density % sol: 49.21 % / Description: NONE
Crystal growpH: 7
Details: HIS6-HOD AT 150 MG/ML IN STORAGE BUFFER IN THE PRESENCE OF A RESERVOIR COMPOSED OF 1.65 M SODIUM/POTASSIUM TARTRATE, 0.1 M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9745
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 23, 2009 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9745 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.51
11-H, L, K20.49
ReflectionResolution: 2.09→53.15 Å / Num. obs: 75553 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.8
Reflection shellResolution: 2.09→2.21 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOD H251A MUTANT SOLVED BY SAD IN SPACE GROUP P 43 21 2 AND NOT FULLY REFINED

Resolution: 2.09→53.16 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.948 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3878 5.2 %TWIN LAW TAKEN INTO ACCOUNT
Rwork0.196 ---
obs0.198 71190 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å20 Å2
2---5.7 Å20 Å2
3---3.71 Å2
Refinement stepCycle: LAST / Resolution: 2.09→53.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8921 0 92 279 9292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0219323
X-RAY DIFFRACTIONr_bond_other_d0.0020.026375
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.94812689
X-RAY DIFFRACTIONr_angle_other_deg1.023.00115387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46451095
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13323.388487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.687151466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4571573
X-RAY DIFFRACTIONr_chiral_restr0.0920.21299
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110433
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021980
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_it0.6241.55464
X-RAY DIFFRACTIONr_mcbond_other0.2081.52191
X-RAY DIFFRACTIONr_mcangle_it1.10728827
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.87233859
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8984.53859
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
1A1575tight positional0.050.05
2B1575tight positional0.050.05
3C1575tight positional0.050.05
4D1575tight positional0.050.05
1A2162loose positional0.055
2B2162loose positional0.045
3C2162loose positional0.045
4D2162loose positional0.045
1A1575tight thermal0.170.5
2B1575tight thermal0.160.5
3C1575tight thermal0.180.5
4D1575tight thermal0.160.5
1A2162loose thermal0.1410
2B2162loose thermal0.1410
3C2162loose thermal0.1410
4D2162loose thermal0.1310
LS refinement shellResolution: 2.09→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 230 -
Rwork0.281 4166 -
obs--77.67 %

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