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- PDB-3fe5: Crystal structure of 3-hydroxyanthranilate 3,4-dioxygenase from b... -

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Basic information

Entry
Database: PDB / ID: 3fe5
TitleCrystal structure of 3-hydroxyanthranilate 3,4-dioxygenase from bovine kidney
Components3-hydroxyanthranilate 3,4-dioxygenase
KeywordsOXIDOREDUCTASE / CUPIN / 3HAO / Quinolinic acid / Cytoplasm / Dioxygenase / Iron / Metal-binding
Function / homology
Function and homology information


quinolinate metabolic process / 3-hydroxyanthranilate 3,4-dioxygenase / 3-hydroxyanthranilate 3,4-dioxygenase activity / anthranilate metabolic process / 'de novo' NAD+ biosynthetic process from L-tryptophan / quinolinate biosynthetic process / L-tryptophan catabolic process / NAD+ biosynthetic process / ferrous iron binding / cytoplasm / cytosol
Similarity search - Function
3-hydroxyanthranilate 3, 4-dioxygenase, metazoan / 3-hydroxyanthranilic acid dioxygenase / 3-hydroxyanthranilic acid dioxygenase / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / 3-hydroxyanthranilate 3,4-dioxygenase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsDilovic, I. / Gliubich, F. / Malpeli, G. / Zanotti, G. / Matkovic-Calogovic, D.
Citation
Journal: Biopolymers / Year: 2009
Title: Crystal structure of bovine 3-hydroxyanthranilate 3,4-dioxygenase.
Authors: Dilovic, I. / Gliubich, F. / Malpeli, G. / Zanotti, G. / Matkovic-Calogovic, D.
#1: Journal: Biochemistry / Year: 2005
Title: Structural studies on 3-hydroxyanthranilate-3,4-dioxygenase: the catalytic mechanism of a complex oxidation involved in NAD biosynthesis.
Authors: Zhang, Y. / Colabroy, K.L. / Begley, T.P. / Ealick, S.E.
#2: Journal: Protein Sci. / Year: 2006
Title: Crystal structure of 3-hydroxyanthranilic acid 3,4-dioxygenase from Saccharomyces cerevisiae: a special subgroup of the type III extradiol dioxygenases.
Authors: Li, X. / Guo, M. / Fan, J. / Tang, W. / Wang, D. / Ge, H. / Rong, H. / Teng, M. / Niu, L. / Liu, Q. / Hao, Q.
History
DepositionNov 27, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5052
Polymers32,4491
Non-polymers561
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.250, 42.520, 46.480
Angle α, β, γ (deg.)91.70, 113.30, 107.70
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 3-hydroxyanthranilate 3,4-dioxygenase / 3-hydroxyanthranilic acid dioxygenase / 3-hydroxyanthranilate oxygenase / 3-HAO


Mass: 32448.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: Q0VCA8, 3-hydroxyanthranilate 3,4-dioxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 40% (NH4)2SO4, Tris-HCl, 40mM MgCl2, 3% MPD, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Jul 27, 1996
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.51→35.07 Å / Num. all: 8486 / Num. obs: 8486 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.2
Reflection shellResolution: 2.51→2.58 Å / Redundancy: 2 % / Rmerge(I) obs: 0.041 / Mean I/σ(I) obs: 3.1 / Num. unique all: 183 / % possible all: 60

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Processing

Software
NameVersionClassification
MAR345data collection
AMoREphasing
REFMAC5.2.0019refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QNK

2qnk


Resolution: 2.51→35.07 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.87 / SU B: 11.378 / SU ML: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24031 399 4.9 %RANDOM
Rwork0.16312 ---
obs0.16689 8486 89.67 %-
all-8486 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.254 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0.01 Å2-0.24 Å2
2--0.12 Å20.05 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.51→35.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 1 55 2326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222327
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9733150
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg17.7245.208288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18323.482112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.98115405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2891521
X-RAY DIFFRACTIONr_chiral_restr0.1060.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021782
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2590.3854
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3330.51517
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.5172
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0380.52
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.333
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.25321438
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.08832276
X-RAY DIFFRACTIONr_scbond_it1.1992999
X-RAY DIFFRACTIONr_scangle_it1.943874
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.515→2.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.497 7 -
Rwork0.236 183 -
obs--28.36 %

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