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- PDB-6bvs: Crystal structure of 3-hydroxyanthranilate-3,4-dioxygenase I142A ... -

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Basic information

Entry
Database: PDB / ID: 6bvs
TitleCrystal structure of 3-hydroxyanthranilate-3,4-dioxygenase I142A from Cupriavidus metallidurans in complex with 4-Cl-3-HAA
Components3-hydroxyanthranilate 3,4-dioxygenase
KeywordsOXIDOREDUCTASE / Complex structure / Dioxygenase / Mutant I142A
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
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: 2.318 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)22,9705
Polymers22,5481
Non-polymers4214
Water1,22568
1
A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)45,93910
Polymers45,0972
Non-polymers8438
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area5310 Å2
ΔGint-63 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.306, 58.306, 230.483
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: 22548.297 Da / Num. of mol.: 1 / Mutation: I142A
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-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
#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: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 8000 13%, 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: 2.31→50 Å / Num. obs: 10918 / % possible obs: 99.9 % / Redundancy: 17.6 % / Biso Wilson estimate: 40.88 Å2 / Rmerge(I) obs: 0.211 / Χ2: 1.09 / Net I/σ(I): 4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.31-2.35190.9335190.538199.8
2.35-2.3918.90.7995270.574199.8
2.39-2.4418.90.7915270.57199.8
2.44-2.4918.90.7335100.5911100
2.49-2.5418.80.6075290.6141100
2.54-2.618.40.6055320.709199.8
2.6-2.6715.60.6415281.441100
2.67-2.74170.495360.7891100
2.74-2.8215.90.3675220.791100
2.82-2.9119.20.3525460.8251100
2.91-3.0119.60.3035220.8851100
3.01-3.1319.10.2615441.131100
3.13-3.2819.10.2365391.311199.8
3.28-3.4516.50.2355441.748199.8
3.45-3.6717.20.2125501.741199.8
3.67-3.9515.10.25471.851199.6
3.95-4.3516.50.1665551.6071100
4.35-4.9818.40.1545741.5831100
4.98-6.2717.50.1435951.3061100
6.27-5014.50.1366721.421199

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YFU

1yfu


Resolution: 2.318→42.197 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.15
RfactorNum. reflection% reflection
Rfree0.2546 1082 10 %
Rwork0.205 --
obs0.2101 10824 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.34 Å2 / Biso mean: 46.1269 Å2 / Biso min: 26.56 Å2
Refinement stepCycle: final / Resolution: 2.318→42.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 22 68 1496
Biso mean--59.26 45.92 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091473
X-RAY DIFFRACTIONf_angle_d0.9012005
X-RAY DIFFRACTIONf_chiral_restr0.053198
X-RAY DIFFRACTIONf_plane_restr0.006269
X-RAY DIFFRACTIONf_dihedral_angle_d17.838859
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3183-2.42380.30141260.21851152127897
2.4238-2.55150.3481310.24621170130199
2.5515-2.71140.36641310.263211791310100
2.7114-2.92070.34591330.251612081341100
2.9207-3.21450.31681340.237512011335100
3.2145-3.67940.25571360.20412161352100
3.6794-4.63480.211380.178312431381100
4.6348-42.20350.20871530.182513731526100

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