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

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Basic information

Entry
Database: PDB / ID: 6bvp
TitleCrystal structure of 3-hydroxyanthranilate-3,4-dioxygenase N27A from Cupriavidus metallidurans
Components3-hydroxyanthranilate 3,4-dioxygenase
KeywordsOXIDOREDUCTASE / Holo structure / Dioxygenase / Mutant N27A
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: 1.903 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 ...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)22,7814
Polymers22,5471
Non-polymers2343
Water2,576143
1
A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)45,5628
Polymers45,0952
Non-polymers4686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_775-y+2,-x+2,-z+1/61
Buried area3980 Å2
ΔGint-48 kcal/mol
Surface area15790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.405, 58.405, 230.507
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-410-

HOH

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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-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.: 143 / 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: 2.52 Å3/Da / Density % sol: 51.13 %
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: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 19292 / % possible obs: 99.4 % / Redundancy: 10.3 % / Biso Wilson estimate: 33.75 Å2 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.051 / Rrim(I) all: 0.167 / Χ2: 1.078 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.975.70.65618160.8740.2760.7170.71597.3
1.97-2.057.50.61118620.910.230.6550.73799.5
2.05-2.149.50.54418860.9530.1830.5750.76199.8
2.14-2.2510.80.42618890.9610.1360.4480.78999.7
2.25-2.39120.34118820.9540.1040.3570.83299.7
2.39-2.5811.90.26419080.9740.0820.2770.88799.6
2.58-2.84110.19719180.9820.0630.2071.06199.7
2.84-3.2512.10.16519700.9840.050.1731.32699.9
3.25-4.0911.20.14919790.9720.0490.1581.66999.8
4.09-5010.70.12721820.9820.0410.1341.53498.9

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Processing

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

1yfu


Resolution: 1.903→42.248 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.88
RfactorNum. reflection% reflection
Rfree0.232 1923 10.01 %
Rwork0.1924 --
obs0.1963 19214 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.32 Å2 / Biso mean: 39.4908 Å2 / Biso min: 24.6 Å2
Refinement stepCycle: final / Resolution: 1.903→42.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1377 0 10 143 1530
Biso mean--47.93 47.2 -
Num. residues----170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071437
X-RAY DIFFRACTIONf_angle_d0.831960
X-RAY DIFFRACTIONf_chiral_restr0.054196
X-RAY DIFFRACTIONf_plane_restr0.005263
X-RAY DIFFRACTIONf_dihedral_angle_d2.5311173
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 (%)
1.9029-1.95050.32231310.27811180131196
1.9505-2.00320.27471300.23411169129999
2.0032-2.06220.22981340.22531196133099
2.0622-2.12870.27981330.20611991332100
2.1287-2.20480.24931350.203512071342100
2.2048-2.29310.28841340.206412161350100
2.2931-2.39740.26121340.197412101344100
2.3974-2.52380.27931390.208212381377100
2.5238-2.68190.23931350.209812231358100
2.6819-2.88890.26091370.200412311368100
2.8889-3.17960.23551390.18112481387100
3.1796-3.63950.19961420.174712771419100
3.6395-4.58440.1971430.161812881431100
4.5844-42.25830.23111570.20551409156699

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