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- PDB-3e9k: Crystal structure of Homo sapiens kynureninase-3-hydroxyhippuric ... -

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Basic information

Entry
Database: PDB / ID: 3e9k
TitleCrystal structure of Homo sapiens kynureninase-3-hydroxyhippuric acid inhibitor complex
ComponentsKynureninase
KeywordsHYDROLASE / kynureninase / kynurenine-L-hydrolase / kynurenine hydrolase / pyridoxal-5'-phosphate / inhibitor complex / 3-hydroxy hippurate / 3-hydroxyhippuric acid / PLP / Pyridine nucleotide biosynthesis / Pyridoxal phosphate
Function / homology
Function and homology information


3-hydroxykynureninase activity / kynureninase / kynureninase activity / response to vitamin B6 / L-kynurenine catabolic process / quinolinate biosynthetic process / anthranilate metabolic process / tryptophan catabolic process to kynurenine / 'de novo' NAD biosynthetic process from tryptophan / Tryptophan catabolism ...3-hydroxykynureninase activity / kynureninase / kynureninase activity / response to vitamin B6 / L-kynurenine catabolic process / quinolinate biosynthetic process / anthranilate metabolic process / tryptophan catabolic process to kynurenine / 'de novo' NAD biosynthetic process from tryptophan / Tryptophan catabolism / tryptophan catabolic process / NAD biosynthetic process / response to type II interferon / pyridoxal phosphate binding / protein homodimerization activity / mitochondrion / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Kynureninase / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Kynureninase / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-Hydroxyhippuric acid / PYRIDOXAL-5'-PHOSPHATE / Kynureninase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLima, S. / Kumar, S. / Gawandi, V. / Momany, C. / Phillips, R.S.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Crystal structure of the Homo sapiens kynureninase-3-hydroxyhippuric acid inhibitor complex: insights into the molecular basis of kynureninase substrate specificity.
Authors: Lima, S. / Kumar, S. / Gawandi, V. / Momany, C. / Phillips, R.S.
History
DepositionAug 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Kynureninase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8833
Polymers52,4401
Non-polymers4422
Water11,385632
1
A: Kynureninase
hetero molecules

A: Kynureninase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7666
Polymers104,8812
Non-polymers8854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6510 Å2
ΔGint-58.2 kcal/mol
Surface area33320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.444, 77.124, 94.558
Angle α, β, γ (deg.)90.00, 109.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-671-

HOH

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Components

#1: Protein Kynureninase / / L-kynurenine hydrolase


Mass: 52440.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KYNU / Plasmid: pCRT7Kyn / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q16719, kynureninase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-3XH / 3-Hydroxyhippuric acid / N-[(3-hydroxyphenyl)carbonyl]glycine


Type: L-peptide linking / Mass: 195.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 632 / 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: 49.63 %
Crystal growTemperature: 298 K / Method: microbatch under oil / pH: 5.12
Details: HKynase solution (9 mg/mL in 50 mM HEPES pH 5.1, and 0.1 mM PLP) mixed (1:1 ratio) with a crystallization solution containing 0.05 M MgCl2, 0.1 M Tris-HCl pH 8.0, 25% PEG 3000, 350 mM HHA, ...Details: HKynase solution (9 mg/mL in 50 mM HEPES pH 5.1, and 0.1 mM PLP) mixed (1:1 ratio) with a crystallization solution containing 0.05 M MgCl2, 0.1 M Tris-HCl pH 8.0, 25% PEG 3000, 350 mM HHA, pH 5.12, MICROBATCH UNDER OIL, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.007 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2007
Details: Rosenbaum-Rock vertical focusing mirror, with Pt, glass, Pd lanes
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 1.7→89.09 Å / Num. all: 51906 / Num. obs: 51906 / % possible obs: 98.55 % / Biso Wilson estimate: 16.68 Å2 / Rsym value: 0.052
Reflection shellResolution: 1.7→1.744 Å / Rsym value: 0.039 / % possible all: 86.66

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HZP

2hzp


Resolution: 1.7→89.09 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.257 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19133 2802 5.1 %RANDOM
Rwork0.1532 ---
obs0.15512 51906 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.686 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-0.87 Å2
2---0.25 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.7→89.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3547 0 29 632 4208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223689
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0651.9744999
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3735450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27824.085164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99915647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5691518
X-RAY DIFFRACTIONr_chiral_restr0.0770.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022766
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.21829
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22532
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.2501
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.89422307
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6553603
X-RAY DIFFRACTIONr_scbond_it2.97371576
X-RAY DIFFRACTIONr_scangle_it4.351101393
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 169 -
Rwork0.22 3370 -
obs--86.66 %
Refinement TLS params.Method: refined / Origin x: 9.8598 Å / Origin y: 0.2047 Å / Origin z: 15.6972 Å
111213212223313233
T-0.0472 Å20.0202 Å20.0018 Å2--0.0248 Å20.0115 Å2---0.0205 Å2
L0.2869 °20.0426 °20.234 °2-0.3583 °20.0069 °2--0.7187 °2
S-0.0629 Å °-0.0388 Å °-0.0382 Å °0.0811 Å °0.0178 Å °-0.0537 Å °-0.0395 Å °0.0669 Å °0.0451 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 37
2X-RAY DIFFRACTION1A38 - 45
3X-RAY DIFFRACTION1A46 - 120
4X-RAY DIFFRACTION1A121 - 190
5X-RAY DIFFRACTION1A191 - 213
6X-RAY DIFFRACTION1A214 - 357
7X-RAY DIFFRACTION1A358 - 375
8X-RAY DIFFRACTION1A376 - 412
9X-RAY DIFFRACTION1A413 - 460

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