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- PDB-6d60: Crystal structure of 3-hydroxyanthranilate-3,4-dioxygenase I142P ... -

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Basic information

Entry
Database: PDB / ID: 6d60
TitleCrystal structure of 3-hydroxyanthranilate-3,4-dioxygenase I142P from Cupriavidus metallidurans
Components3-hydroxyanthranilate 3,4-dioxygenase
KeywordsOXIDOREDUCTASE / Holo structure / Dioxygenase / Mutant I142P
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 / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsYang, Y. / Liu, F. / Liu, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108988 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R21MH107985 United States
National Science Foundation (NSF, United States)CHE-1623856 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Adapting to oxygen: 3-Hydroxyanthrinilate 3,4-dioxygenase employs loop dynamics to accommodate two substrates with disparate polarities.
Authors: Yang, Y. / Liu, F. / Liu, A.
History
DepositionApr 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,8084
Polymers22,5741
Non-polymers2343
Water2,594144
1
A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)45,6168
Polymers45,1492
Non-polymers4686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area4320 Å2
ΔGint-52 kcal/mol
Surface area15790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.472, 58.472, 232.243
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: 22574.334 Da / Num. of mol.: 1 / Mutation: I142P
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 BL21(DE3) (bacteria)
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.: 144 / 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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000 11 %, 100 mM Tris-HCl, 200 mM MgCl2, 1 mM DTT, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. obs: 12593 / % possible obs: 99.8 % / Redundancy: 22.5 % / Biso Wilson estimate: 32.51 Å2 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.039 / Rrim(I) all: 0.188 / Χ2: 1.02 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.22-2.2622.60.9546200.9520.2040.9761.247100
2.26-2.323.51.2575860.9950.2651.2860.97100
2.3-2.3423.60.9836210.9630.2051.0050.951100
2.34-2.3923.50.8355860.970.1750.8530.981100
2.39-2.4423.20.7516250.9790.1580.7680.984100
2.44-2.523.50.6975940.9810.1460.7121.011100
2.5-2.5623.30.5886150.9890.1240.6011.014100
2.56-2.6323.50.5596080.9760.1170.5711.03100
2.63-2.7122.70.516220.9850.1090.5221.145100
2.71-2.823.30.4086160.990.0860.4171.056100
2.8-2.923.20.3416130.9880.0720.3491.05100
2.9-3.0122.90.2946220.9930.0620.3011.058100
3.01-3.1523.10.2176200.9970.0460.2221.076100
3.15-3.3222.60.1586270.9980.0340.1611.045100
3.32-3.5222.50.146370.9980.030.1431.106100
3.52-3.822.30.1266360.9980.0270.1291.103100
3.8-4.1821.80.1026570.9980.0220.1041.016100
4.18-4.7821.80.086480.9990.0180.0820.848100
4.78-6.0221.10.0856820.9990.0180.0870.793100
6.02-5018.30.0837580.9980.020.0860.92397.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YFU

1yfu


Resolution: 2.22→34.23 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.42
RfactorNum. reflection% reflection
Rfree0.2516 1251 10.01 %
Rwork0.208 --
obs0.2125 12499 99.77 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 34.636 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso max: 70.75 Å2 / Biso mean: 35.5216 Å2 / Biso min: 19.03 Å2
Baniso -1Baniso -2Baniso -3
1-9.015 Å2-0 Å2-0 Å2
2--9.015 Å2-0 Å2
3----18.03 Å2
Refinement stepCycle: final / Resolution: 2.22→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 10 144 1562
Biso mean--40.97 37.79 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081463
X-RAY DIFFRACTIONf_angle_d1.1741993
X-RAY DIFFRACTIONf_chiral_restr0.076198
X-RAY DIFFRACTIONf_plane_restr0.006268
X-RAY DIFFRACTIONf_dihedral_angle_d14.182544
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2179-2.30670.33751340.29451208134299
2.3067-2.41170.3091360.244212131349100
2.4117-2.53880.35441340.257812111345100
2.5388-2.69780.30231340.245912051339100
2.6978-2.9060.29421380.247512401378100
2.906-3.19820.29041370.225212341371100
3.1982-3.66050.23231410.215612611402100
3.6605-4.61010.22141420.162912781420100
4.6101-34.23370.19491550.176813981553100

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