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- PDB-1yfu: Crystal structure of 3-hydroxyanthranilate-3,4-dioxygenase from R... -

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Basic information

Entry
Database: PDB / ID: 1yfu
TitleCrystal structure of 3-hydroxyanthranilate-3,4-dioxygenase from Ralstonia metallidurans
Components3-hydroxyanthranilate-3,4-dioxygenase
KeywordsOXIDOREDUCTASE / cupin
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
: / : / 3-hydroxyanthranilate 3,4-dioxygenase
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, molecular replacement / Resolution: 1.9 Å
AuthorsZhang, Y. / Colabroy, K.L. / Begley, T.P. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2005
Title: Structural Studies on 3-Hydroxyanthranilate-3,4-dioxygenase: The Catalytic Mechanism of a Complex Oxidation Involved in NAD Biosynthesis.
Authors: Zhang, Y. / Colabroy, K.L. / Begley, T.P. / Ealick, S.E.
History
DepositionJan 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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 / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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)20,3265
Polymers20,0571
Non-polymers2694
Water2,756153
1
A: 3-hydroxyanthranilate-3,4-dioxygenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)40,65210
Polymers40,1132
Non-polymers5398
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area4500 Å2
ΔGint-72 kcal/mol
Surface area16050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.100, 58.100, 230.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe second part of the biological assembly is generated by the two fold axis: -y + 1, -x + 1, -z + 1/6

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Components

#1: Protein 3-hydroxyanthranilate-3,4-dioxygenase


Mass: 20056.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / Production host: Escherichia coli (E. coli)
References: GenBank: 48769986, UniProt: Q1LCS4*PLUS, 3-hydroxyanthranilate 3,4-dioxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 8-BM10.9792
SYNCHROTRONCHESS A120.9769
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97691
ReflectionResolution: 1.9→42.11 Å / Num. all: 18779 / Num. obs: 17369 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.3 Å2
Reflection shellResolution: 1.9→2.02 Å / % possible all: 72.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: SAD, molecular replacement / Resolution: 1.9→42.11 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 302680.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 839 4.8 %RANDOM
Rwork0.216 ---
all0.216 18779 --
obs0.216 17369 90.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.1936 Å2 / ksol: 0.387155 e/Å3
Displacement parametersBiso mean: 38.4 Å2
Baniso -1Baniso -2Baniso -3
1-8.38 Å25.16 Å20 Å2
2--8.38 Å20 Å2
3----16.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.9→42.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 11 153 1573
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.962.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 115 5.1 %
Rwork0.307 2138 -
obs--72.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2LIGANDS.PARAMLIGANDS.TOP
X-RAY DIFFRACTION3WATER.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAMWATER.TOP

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