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- PDB-6bvq: Crystal structure of 3-hydroxyanthranilate-3,4-dioxygenase N27A f... -

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Basic information

Entry
Database: PDB / ID: 6bvq
TitleCrystal structure of 3-hydroxyanthranilate-3,4-dioxygenase N27A from Cupriavidus metallidurans in complex with 4-Cl-3-HAA
Components3-hydroxyanthranilate 3,4-dioxygenase
KeywordsOXIDOREDUCTASE / Complex structure / Dioxygenase / Mutant N27A
Function / homology
Function and homology information


3-hydroxyanthranilate 3,4-dioxygenase / 3-hydroxyanthranilate 3,4-dioxygenase activity / quinolinate biosynthetic process / anthranilate metabolic process / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / ferrous iron binding / cytoplasm
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: 2.084 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 Mental Health (NIH/NIMH)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
DepositionDec 13, 2017Deposition 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 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,9695
Polymers22,5471
Non-polymers4214
Water1,72996
1
A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)45,93810
Polymers45,0952
Non-polymers8438
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area5030 Å2
ΔGint-64 kcal/mol
Surface area15350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.608, 58.608, 236.316
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: 22547.352 Da / Num. of mol.: 1 / Mutation: N27A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / 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.: 96 / 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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 8000 15%, 0.1M Tris-HCl, 0.2 M MgCl2, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.084→50 Å / Num. obs: 14268 / % possible obs: 94.3 % / Redundancy: 28.7 % / Biso Wilson estimate: 39.58 Å2 / Rmerge(I) obs: 0.236 / Χ2: 1.059 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.1-2.1831.40.39414660.8391100
2.18-2.2630.50.37214551.081199.9
2.26-2.3732.80.35414641.164199.6
2.37-2.4933.80.30614551.0381100
2.49-2.6533.60.2914671.12199.8
2.65-2.85280.2814941.198199.7
2.85-3.1431.90.2614791.14198.5
3.14-3.5922.10.24712951.157185.6
3.59-4.5215.70.22711111.058170.6
4.52-5023.40.20315820.777191.4

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Processing

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

1yfu


Resolution: 2.084→31.116 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.78
RfactorNum. reflection% reflection
Rfree0.2671 1420 10.01 %
Rwork0.2281 --
obs0.232 14192 92.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.26 Å2 / Biso mean: 44.7565 Å2 / Biso min: 25.46 Å2
Refinement stepCycle: final / Resolution: 2.084→31.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1377 0 22 99 1498
Biso mean--51.69 48.1 -
Num. residues----170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111448
X-RAY DIFFRACTIONf_angle_d0.9351967
X-RAY DIFFRACTIONf_chiral_restr0.057195
X-RAY DIFFRACTIONf_plane_restr0.006263
X-RAY DIFFRACTIONf_dihedral_angle_d7.438838
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.084-2.15850.40581210.27241094121582
2.1585-2.24490.29031480.256713211469100
2.2449-2.3470.33431490.262113441493100
2.347-2.47070.34151480.243913331481100
2.4707-2.62540.35131490.247113341483100
2.6254-2.8280.28261510.23613701521100
2.828-3.11240.30381500.251350150099
3.1124-3.56220.26841330.24751192132586
3.5622-4.48590.24541130.21741017113071
4.4859-31.11990.20721580.1941417157592

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