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- PDB-5v26: 1.78 angstrom crystal structure of P97H 3-hydroxyanthranilate-3,4... -

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Basic information

Entry
Database: PDB / ID: 5v26
Title1.78 angstrom crystal structure of P97H 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 / 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: 1.79 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: 1.78 angstrom crystal structure of P97H 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,4656
Polymers46,2422
Non-polymers2234
Water4,864270
1
A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2333
Polymers23,1211
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2333
Polymers23,1211
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.229, 57.692, 79.501
Angle α, β, γ (deg.)90.000, 103.820, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-hydroxyanthranilate 3,4-dioxygenase / 3-hydroxyanthranilate oxygenase / 3-HAO / 3-hydroxyanthranilic acid dioxygenase / HAD


Mass: 23120.945 Da / Num. of mol.: 2
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.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
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: Aug 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 37328 / % possible obs: 98.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 26.59 Å2 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.05 / Rrim(I) all: 0.139 / Χ2: 1.133 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.79-1.855.70.7970.7870.3430.870.72589.6
1.85-1.936.80.6590.8840.2680.7130.7899.1
1.93-2.027.40.4760.9390.1870.5120.853100
2.02-2.127.60.3550.9650.1370.3810.918100
2.12-2.267.60.2670.9780.1030.2871.017100
2.26-2.437.60.220.9780.0850.2361.143100
2.43-2.677.60.1780.9860.0690.191.233100
2.67-3.067.70.1440.9870.0560.1551.345100
3.06-3.867.60.1240.9880.0480.1331.841100
3.86-507.50.0840.9940.0330.091.25199.9

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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: 1.79→38.6 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.29
RfactorNum. reflection% reflection
Rfree0.24 1868 5.01 %
Rwork0.1979 --
obs0.2 37287 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.84 Å2 / Biso mean: 35.3916 Å2 / Biso min: 17.02 Å2
Refinement stepCycle: final / Resolution: 1.79→38.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 4 270 3067
Biso mean--33.38 38.84 -
Num. residues----343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072887
X-RAY DIFFRACTIONf_angle_d0.8873930
X-RAY DIFFRACTIONf_chiral_restr0.057393
X-RAY DIFFRACTIONf_plane_restr0.006528
X-RAY DIFFRACTIONf_dihedral_angle_d5.351690
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7891-1.83750.29921270.2972433256090
1.8375-1.89160.32411550.27872682283797
1.8916-1.95260.30541390.244827082847100
1.9526-2.02240.26951310.238127282859100
2.0224-2.10340.28411360.23127842920100
2.1034-2.19910.31631650.224527052870100
2.1991-2.3150.27371450.220227382883100
2.315-2.460.29191330.226527652898100
2.46-2.64990.27651470.227527572904100
2.6499-2.91650.27531800.222127172897100
2.9165-3.33840.24261220.205827762898100
3.3384-4.20520.20831500.17127832933100
4.2052-38.60860.16821380.148628432981100

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