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- PDB-5v28: 2.72 angstrom crystal structure of P97A 3-hydroxyanthranilate-3,4... -

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Basic information

Entry
Database: PDB / ID: 5v28
Title2.72 angstrom crystal structure of P97A 3-hydroxyanthranilate-3,4-dioxygenase from Cupriavidus metallidurans
Components3-hydroxyanthranilate 3,4-dioxygenase
KeywordsOXIDOREDUCTASE / HAO Kynurenine Cupin 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
: / 3-hydroxyanthranilate 3,4-dioxygenase
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.724 Å
AuthorsDornevil, K. / Liu, F. / Liu, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1623856 United States
CitationJournal: To Be Published
Title: 2.72 angstrom crystal structure of P97A 3-hydroxyanthranilate-3,4-dioxygenase from Cupriavidus metallidurans
Authors: Dornevil, K. / Liu, F. / Liu, A.
History
DepositionMar 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)23,2884
Polymers23,0541
Non-polymers2343
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.602, 58.602, 231.523
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 23053.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34) (bacteria)
Strain: ATCC 43123 / DSM 2839 / NBRC 102507 / CH34 / 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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris-HCl, 200 mM MgCl2, 20% PEG 8000, and 1 mM DTT, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.72→50 Å / Num. obs: 6174 / % possible obs: 87.9 % / Redundancy: 23.6 % / Biso Wilson estimate: 47.19 Å2 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.036 / Rrim(I) all: 0.191 / Χ2: 1.004 / Net I/σ(I): 5 / Num. measured all: 145783
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.72-2.824.60.5140.8280.2070.560.68836.6
2.82-2.937.20.5880.8470.1850.6210.75956.3
2.93-3.0610.40.5380.9260.1420.560.79985.4
3.06-3.22150.4480.9440.1050.4620.84696.6
3.22-3.4322.50.3820.9880.0780.390.956100
3.43-3.6928.70.3040.9940.0560.3090.957100
3.69-4.0632.20.2490.9950.0440.2531.023100
4.06-4.6532.30.1620.9970.0290.1651.008100
4.65-5.8631.50.1410.9980.0250.1430.974100
5.86-5027.60.1120.9990.0220.1141.24299

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHENIXphasing
RefinementResolution: 2.724→34.206 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.54
RfactorNum. reflection% reflection
Rfree0.2618 279 4.57 %
Rwork0.1922 --
obs0.1956 6099 87.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.02 Å2 / Biso mean: 43.2591 Å2 / Biso min: 22.05 Å2
Refinement stepCycle: final / Resolution: 2.724→34.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 0 22 10 1439
Biso mean--59.62 35.43 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011460
X-RAY DIFFRACTIONf_angle_d1.0951987
X-RAY DIFFRACTIONf_chiral_restr0.053199
X-RAY DIFFRACTIONf_plane_restr0.005266
X-RAY DIFFRACTIONf_dihedral_angle_d18.07857
LS refinement shellResolution: 2.724→3.4314 Å / Rfactor Rfree error: 0 / Total num. of bins used: 2
RfactorNum. reflection% reflection
Rfree0.3852 106 -
Rwork0.2527 2397 -
all-2503 -
obs--75 %

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