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- PDB-6d62: Crystal structure of 3-hydroxyanthranilate-3,4-dioxygenase I142P ... -

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Basic information

Entry
Database: PDB / ID: 6d62
TitleCrystal structure of 3-hydroxyanthranilate-3,4-dioxygenase I142P from Cupriavidus metallidurans in complex with 3-HAA
Components3-hydroxyanthranilate 3,4-dioxygenase
KeywordsOXIDOREDUCTASE / Holo structure / Dioxygenase / Mutant I142P / 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
3-HYDROXYANTHRANILIC ACID / : / 3-hydroxyanthranilate 3,4-dioxygenase
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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)R21MH10798 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)22,9615
Polymers22,5741
Non-polymers3874
Water5,332296
1
A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)45,92310
Polymers45,1492
Non-polymers7748
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area5120 Å2
ΔGint-42 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.881, 58.881, 232.305
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-539-

HOH

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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-3HA / 3-HYDROXYANTHRANILIC ACID / 2-AMINO-3-HYDROXYBENZOIC ACID


Mass: 153.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO3 / 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.: 296 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
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 8.50

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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: 1.77→50 Å / Num. obs: 24171 / % possible obs: 98.6 % / Redundancy: 9.9 % / Biso Wilson estimate: 20.42 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.028 / Rrim(I) all: 0.087 / Χ2: 1.187 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.77-1.890.31411510.9690.1090.3330.66597.9
1.8-1.839.30.27911900.9760.0950.2960.71299
1.83-1.8710.10.25311560.9820.0840.2670.7899.7
1.87-1.9110.50.27512010.9830.0890.290.9299.5
1.91-1.9510.30.25211780.9830.0820.2651.2299.7
1.95-1.9910.50.18811860.9890.0610.1981.01199.7
1.99-2.0410.50.16912030.9890.0550.1781.04499.8
2.04-2.110.20.17611930.9880.0580.1861.30799.7
2.1-2.1610.40.13911840.9920.0450.1461.18399.7
2.16-2.2310.40.12812000.9930.0420.1351.22999.8
2.23-2.31100.13212030.9930.0440.1391.4999.7
2.31-2.410.40.10812020.9950.0350.1141.29499.7
2.4-2.5110.40.112140.9960.0320.1051.297100
2.51-2.6410.40.09112270.9950.0290.0961.3199.8
2.64-2.8110.20.08312260.9970.0270.0881.426100
2.81-3.0310.20.07312340.9970.0240.0761.3399.8
3.03-3.33100.06412440.9970.0210.0671.44499.7
3.33-3.819.10.0612300.9970.0210.0641.46297
3.81-4.88.20.05412190.9970.020.0581.33993.8
4.8-508.20.05413300.9970.0190.0581.18591.2

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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: 1.77→29.441 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.18
RfactorNum. reflection% reflection
Rfree0.216 1997 8.28 %
Rwork0.1868 --
obs0.1892 24111 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.38 Å2 / Biso mean: 23.9018 Å2 / Biso min: 11.92 Å2
Refinement stepCycle: final / Resolution: 1.77→29.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 21 298 1727
Biso mean--26.4 33.04 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061481
X-RAY DIFFRACTIONf_angle_d0.8482019
X-RAY DIFFRACTIONf_chiral_restr0.056199
X-RAY DIFFRACTIONf_plane_restr0.006272
X-RAY DIFFRACTIONf_dihedral_angle_d8.0921213
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 (%)
1.7695-1.81370.24121360.19751505164198
1.8137-1.86280.23151400.199715541694100
1.8628-1.91760.2711410.220715511692100
1.9176-1.97940.24791400.201415541694100
1.9794-2.05020.23831410.187515621703100
2.0502-2.13220.20861420.191615711713100
2.1322-2.22920.22351410.186915531694100
2.2292-2.34670.25041420.215751717100
2.3467-2.49370.25821440.194315801724100
2.4937-2.68610.23411430.204716081751100
2.6861-2.95620.24981450.198116001745100
2.9562-3.38340.19211460.182116181764100
3.3834-4.26070.18541430.16711601174496
4.2607-29.44460.18341530.17341682183593

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