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- PDB-5v27: 2.35 angstrom crystal structure of P97V 3-hydroxyanthranilate-3,4... -

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Basic information

Entry
Database: PDB / ID: 5v27
Title2.35 angstrom crystal structure of P97V 3-hydroxyanthranilate-3,4-dioxygenase from Cupriavidus metallidurans
Components3-hydroxyanthranilate 3,4-dioxygenase
KeywordsOXIDOREDUCTASE / HAO Kynurenine Cupin Dioxygenase
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
: / 3-hydroxyanthranilate 3,4-dioxygenase
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.352 Å
AuthorsDornevil, K. / Liu, F. / Liu, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1623856 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R21MH107985 United States
CitationJournal: To Be Published
Title: 2.35 angstrom crystal structure of P97V 3-hydroxyanthranilate-3,4-dioxygenase from Cupriavidus metallidurans
Authors: Dornevil, K. / Liu, F. / Liu, A.
History
DepositionMar 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
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)23,3164
Polymers23,0821
Non-polymers2343
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.032, 58.032, 231.868
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: 23081.930 Da / Num. of mol.: 1
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 (E. coli)
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
#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.: 15 / 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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris-HCl, 200 mM MgCl2, 20% PEG 8000, and 1 mM DTT, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 10362 / % possible obs: 98.7 % / Redundancy: 27.6 % / Biso Wilson estimate: 46.63 Å2 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.026 / Rrim(I) all: 0.129 / Χ2: 1.102 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.4324.80.5460.990.1060.5560.741100
2.43-2.5330.10.5610.9960.1030.5710.758100
2.53-2.6533.50.4960.9960.0870.5040.799100
2.65-2.7933.40.3840.9960.0680.390.88199.9
2.79-2.9632.50.3080.9960.0550.3131.01199.9
2.96-3.1930.60.2060.9970.0390.211.17399.3
3.19-3.5127.30.1340.9980.0270.1371.30698.8
3.51-4.0224.50.0990.9980.0220.1021.45296.6
4.02-5.0619.20.0810.9970.020.0841.73895.2
5.06-5021.30.0620.9980.0140.0641.55198

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Processing

Software
NameVersionClassification
PHENIXrefinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YFU

1yfu


Resolution: 2.352→37.973 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2744 522 5.09 %
Rwork0.2093 9724 -
obs0.2125 10246 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.46 Å2 / Biso mean: 56.5695 Å2 / Biso min: 34.67 Å2
Refinement stepCycle: final / Resolution: 2.352→37.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 22 15 1446
Biso mean--71.73 51.67 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071462
X-RAY DIFFRACTIONf_angle_d0.821990
X-RAY DIFFRACTIONf_chiral_restr0.05200
X-RAY DIFFRACTIONf_plane_restr0.006266
X-RAY DIFFRACTIONf_dihedral_angle_d15.497858
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3521-2.58880.30261120.24742364247699
2.5888-2.96320.34991300.2724072537100
2.9632-3.73290.29921410.24162383252498
3.7329-37.97750.23681390.17542570270997

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