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- PDB-6d61: Crystal structure of 3-hydroxyanthranilate-3,4-dioxygenase I142P ... -

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Basic information

Entry
Database: PDB / ID: 6d61
TitleCrystal structure of 3-hydroxyanthranilate-3,4-dioxygenase I142P from Cupriavidus metallidurans in complex with 4-Cl-3-HAA
Components3-hydroxyanthranilate 3,4-dioxygenase
KeywordsOXIDOREDUCTASE / Complex structure / Dioxygenase / Mutant I142P / 4-Cl-3-HAA
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
4-CHLORO-3-HYDROXYANTHRANILIC ACID / : / 3-hydroxyanthranilate 3,4-dioxygenase
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsYang, Y. / Liu, F. / Liu, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)R01GM108988 United States
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)22,9965
Polymers22,5741
Non-polymers4214
Water4,756264
1
A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)45,99110
Polymers45,1492
Non-polymers8438
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area5210 Å2
ΔGint-63 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.701, 58.701, 231.896
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-4AA / 4-CHLORO-3-HYDROXYANTHRANILIC ACID / 2-AMINO-4-CHLORO-3-HYDROXYBENZOIC ACID


Mass: 187.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6ClNO3 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000 10%, 1 mM DTT, 100 mM Tris-HCl, 200 mM MgCl2, 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: 1.74→50 Å / Num. obs: 25473 / % possible obs: 99.5 % / Redundancy: 26.1 % / Biso Wilson estimate: 23.11 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.02 / Rrim(I) all: 0.103 / Χ2: 1.056 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.74-1.7721.20.90911600.9520.1990.9310.5892.9
1.77-1.823.60.73312260.9770.1530.7490.597100
1.8-1.84250.65612730.9820.1330.670.643100
1.84-1.8727.40.62812180.9870.1220.640.684100
1.87-1.9226.70.75512410.9820.1490.771.13100
1.92-1.9626.30.64112670.9860.1280.6541.3499.8
1.96-2.0128.40.36712240.9930.070.3740.831100
2.01-2.0627.70.3312490.9960.0640.3360.922100
2.06-2.1227.30.29512560.9940.0570.3011.115100
2.12-2.1928.30.22512530.9970.0430.230.997100
2.19-2.2724.80.26212650.9950.0550.2681.504100
2.27-2.36280.18112660.9970.0350.1851.1199.9
2.36-2.4727.80.1512720.9980.0290.1521.099100
2.47-2.6280.13312640.9980.0260.1351.142100
2.6-2.7627.40.11412780.9990.0220.1161.28100
2.76-2.9827.40.09312970.9960.0180.0951.244100
2.98-3.2727.10.07313140.9990.0140.0741.27100
3.27-3.7524.20.06313140.9990.0130.0651.359100
3.75-4.7223.40.05213600.9990.0110.0531.12199.9
4.72-5022.70.04814760.9990.010.050.95597.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YFU

1yfu


Resolution: 1.74→29.351 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 1979 7.91 %
Rwork0.1987 23038 -
obs0.2017 25017 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.61 Å2 / Biso mean: 29.1095 Å2 / Biso min: 16.2 Å2
Refinement stepCycle: final / Resolution: 1.74→29.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 22 264 1694
Biso mean--30.85 37.83 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061475
X-RAY DIFFRACTIONf_angle_d0.8022010
X-RAY DIFFRACTIONf_chiral_restr0.052198
X-RAY DIFFRACTIONf_plane_restr0.005270
X-RAY DIFFRACTIONf_dihedral_angle_d11.195867
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7398-1.78330.2931380.2211615175398
1.7833-1.83150.2591380.215516091747100
1.8315-1.88540.34481390.223916271766100
1.8854-1.94630.43391250.34321383150886
1.9463-2.01580.2641400.222216441784100
2.0158-2.09650.24831400.22671645178599
2.0965-2.19190.26281380.214616121750100
2.1919-2.30740.3031370.25751582171995
2.3074-2.45190.28211420.214816641806100
2.4519-2.64110.26081420.220116551797100
2.6411-2.90670.23581450.204916841829100
2.9067-3.32680.19991450.187717021847100
3.3268-4.18950.211500.165617421892100
4.1895-29.35470.19021600.16781874203499

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