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- PDB-4wzc: Understanding Extradiol Dioxygenase Mechanism in NAD+ Biosynthesi... -

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Basic information

Entry
Database: PDB / ID: 4wzc
TitleUnderstanding Extradiol Dioxygenase Mechanism in NAD+ Biosynthesis by Viewing Catalytic Intermediates - 2,3-cis-4,5-trans ACMS bound to I142A mutant HAO
Components3-hydroxyanthranilate 3,4-dioxygenase
KeywordsOXIDOREDUCTASE / bi-cupin iron-binding / dioxygenase
Function / homology
Function and homology information


3-hydroxyanthranilate 3,4-dioxygenase / 3-hydroxyanthranilate 3,4-dioxygenase activity / anthranilate metabolic process / quinolinate biosynthetic process / L-tryptophan catabolic process / NAD+ biosynthetic process / ferrous iron binding
Similarity search - Function
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
Chem-1UC / : / 3-hydroxyanthranilate 3,4-dioxygenase
Similarity search - Component
Biological speciesRalstonia metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.842 Å
AuthorsLiu, F. / Liu, A.
CitationJournal: To Be Published
Title: Probing Extradiol Dioxygenase Mechanism in NAD+ Biosynthesis by Viewing Reaction Cycle Intermediates
Authors: Liu, F. / Liu, A.
History
DepositionNov 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Non-polymer description
Revision 1.2Aug 9, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)20,7264
Polymers20,4291
Non-polymers2973
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.282, 58.282, 230.605
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 20428.996 Da / Num. of mol.: 1 / Mutation: I142A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia metallidurans (bacteria) / Strain: CH34 / ATCC 43123 / DSM 2839 / Gene: nbaC, Rmet_5193 / Production host: Escherichia coli (E. coli)
References: UniProt: Q1LCS4, 3-hydroxyanthranilate 3,4-dioxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-1UC / (2E)-2-amino-3-[(1E)-3-oxoprop-1-en-1-yl]but-2-enedioic acid


Mass: 185.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: PEG 8000

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Data collection

DiffractionMean temperature: 191 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 21142 / % possible obs: 87.9 % / Redundancy: 17.6 % / Net I/σ(I): 56.47

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 4R52

4r52


Resolution: 1.842→34.047 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 947 5.11 %Random selection
Rwork0.2046 ---
obs0.2071 18518 87.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.842→34.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1403 15 98 1516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0231475
X-RAY DIFFRACTIONf_angle_d1.6562015
X-RAY DIFFRACTIONf_dihedral_angle_d12.67538
X-RAY DIFFRACTIONf_chiral_restr0.084201
X-RAY DIFFRACTIONf_plane_restr0.008269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8423-1.93950.2964800.22631360X-RAY DIFFRACTION49
1.9395-2.0610.27311090.21681973X-RAY DIFFRACTION72
2.061-2.22010.26881480.21142622X-RAY DIFFRACTION94
2.2201-2.44340.28591530.20232818X-RAY DIFFRACTION100
2.4434-2.79690.25251540.21742830X-RAY DIFFRACTION100
2.7969-3.52320.2711480.21212870X-RAY DIFFRACTION99
3.5232-34.05330.24231550.19493098X-RAY DIFFRACTION99

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