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

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Basic information

Entry
Database: PDB / ID: 6bvr
TitleCrystal structure of 3-hydroxyanthranilate-3,4-dioxygenase I142A from Cupriavidus metallidurans
Components3-hydroxyanthranilate 3,4-dioxygenase
KeywordsOXIDOREDUCTASE / Holo structure / Dioxygenase / Mutant I142A
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: 1.9 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)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
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 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)22,7824
Polymers22,5481
Non-polymers2343
Water3,261181
1
A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)45,5648
Polymers45,0972
Non-polymers4686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area4360 Å2
ΔGint-52 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.914, 58.914, 232.062
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-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
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 8000 14%, 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: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 20024 / % possible obs: 99.9 % / Redundancy: 10.8 % / Biso Wilson estimate: 32.01 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.038 / Rrim(I) all: 0.124 / Χ2: 1.076 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.938.20.3829460.9680.1350.4060.56899.3
1.93-1.979.80.399830.9720.130.4120.54499.8
1.97-2.0110.70.3499560.9830.1110.3670.55599.8
2.01-2.0511.20.3299800.9860.1030.3460.58699.8
2.05-2.0911.30.3169540.9860.10.3320.72299.9
2.09-2.1411.30.2849770.9870.0880.2970.66699.9
2.14-2.1911.40.259720.9880.0790.2630.75999.9
2.19-2.2511.20.2279730.9910.0720.2390.823100
2.25-2.3211.10.229860.9910.0690.2310.89899.9
2.32-2.3910.60.1929830.9860.0620.2020.988100
2.39-2.489.70.1739970.9920.0570.1831.05999.9
2.48-2.5811.80.1749840.990.0540.1821.14100
2.58-2.711.60.16410060.9940.0510.1721.263100
2.7-2.8411.60.1529880.9930.0470.161.41599.9
2.84-3.0211.30.1459940.9910.0450.1521.47299.6
3.02-3.2511.10.1310160.9930.0410.1371.6899.8
3.25-3.589.60.11310120.9950.0380.121.705100
3.58-4.0911.20.10810490.9950.0340.1131.64100
4.09-5.1610.90.10310710.9950.0320.1081.534100
5.16-509.50.08311970.9980.0280.0881.17499.6

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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 / Resolution: 1.9→42.591 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.9
RfactorNum. reflection% reflection
Rfree0.2411 1989 10.01 %
Rwork0.1923 --
obs0.1972 19877 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.72 Å2 / Biso mean: 40.5602 Å2 / Biso min: 25.17 Å2
Refinement stepCycle: final / Resolution: 1.9→42.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 10 181 1597
Biso mean--38.64 46.54 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071487
X-RAY DIFFRACTIONf_angle_d0.8962031
X-RAY DIFFRACTIONf_chiral_restr0.056201
X-RAY DIFFRACTIONf_plane_restr0.006273
X-RAY DIFFRACTIONf_dihedral_angle_d15.022877
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 (%)
1.8958-1.94320.32951340.25741207134198
1.9432-1.99570.23961370.23821233137099
1.9957-2.05440.28341380.21571238137699
2.0544-2.12070.271390.20421245138499
2.1207-2.19650.23621370.20171243138099
2.1965-2.28450.26491390.20791253139299
2.2845-2.38840.32091400.215712571397100
2.3884-2.51440.28571400.212912581398100
2.5144-2.67190.2791430.217712791422100
2.6719-2.87810.27371400.202812691409100
2.8781-3.16770.26641430.21812921435100
3.1677-3.62580.22421460.189413141460100
3.6258-4.56730.19021500.163313391489100
4.5673-42.60160.2291630.175314611624100

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