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- PDB-1qz9: The Three Dimensional Structure of Kynureninase from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 1qz9
TitleThe Three Dimensional Structure of Kynureninase from Pseudomonas fluorescens
ComponentsKYNURENINASE
KeywordsHYDROLASE / kynurenine / tryptophan / PLP / vitamin B6 / pyridoxal-5'-phosphate
Function / homology
Function and homology information


kynureninase / kynureninase activity / L-kynurenine catabolic process / anthranilate metabolic process / L-tryptophan catabolic process to L-kynurenine / quinolinate biosynthetic process / NAD+ biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Kynureninase / Kynureninase C-terminal domain / DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / 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 ...Kynureninase / Kynureninase C-terminal domain / DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / 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
3,6,9,12,15-PENTAOXAHEPTADECANE / PYRIDOXAL-5'-PHOSPHATE / Kynureninase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / MIR, molecular replacement / Resolution: 1.85 Å
AuthorsMomany, C. / Levdikov, V. / Blagova, L. / Lima, S. / Phillips, R.S.
CitationJournal: Biochemistry / Year: 2004
Title: Three-Dimensional Structure of Kynureninase from Pseudomonas fluorescens.
Authors: Momany, C. / Levdikov, V. / Blagova, L. / Lima, S. / Phillips, R.S.
History
DepositionSep 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 23, 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
Remark 600HETEROGEN THE LIGAND P3G IS A POLYETHYLENE GLYCOL POLYMER (POSSIBLY MYRISTIC ACID).
Remark 999SEQUENCE NO SEQUENCE DATABASE REFERENCE WAS AVAILABLE FOR THIS PROTEIN AT THE TIME OF PROCESSING. ...SEQUENCE NO SEQUENCE DATABASE REFERENCE WAS AVAILABLE FOR THIS PROTEIN AT THE TIME OF PROCESSING. THE SEQUENCE IS DESCRIBED IN CLONING, SEQUENCE, AND EXPRESSION OF KYNURENINASE FROM PSEUDOMONAS FLUORESCENS. KOUSHIK SV, SUNDARARAJU B, MCGRAW RA, PHILLIPS RS. ARCH BIOCHEM BIOPHYS. 1997, V.344, PGS.301-8.

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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)46,4834
Polymers45,9501
Non-polymers5333
Water7,710428
1
A: KYNURENINASE
hetero molecules

A: KYNURENINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9668
Polymers91,9002
Non-polymers1,0666
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area9140 Å2
ΔGint-85 kcal/mol
Surface area27460 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.076, 68.076, 137.976
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological unit is a dimer generated by applying the symmetry operator (X-Y,-Y,2/3-Z) translated by 1 unit along the b axis

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Components

#1: Protein KYNURENINASE


Mass: 45949.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Plasmid: pTZ18U / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P83788, kynureninase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-P3G / 3,6,9,12,15-PENTAOXAHEPTADECANE


Mass: 250.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.01 Å3/Da / Density % sol: 38.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: lithium chloride, PEG 400, potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Jancarik, J., (1991) J. Appl. Crystallogr., 24, 409.
Components of the solutions
*PLUS
Conc.: 10 mg/ml / Common name: protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→58.72 Å / Num. obs: 29707 / % possible obs: 96.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 13.9 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 25.4
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2 / Num. unique all: 1465 / % possible all: 92.9
Reflection
*PLUS
Lowest resolution: 58.7 Å

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR, molecular replacement
Starting model: PDB ENTRY 1C0N

1c0n


Resolution: 1.85→19.65 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.057 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC REFINEMENT WITH TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.142 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19154 1576 5 %RANDOM
Rwork0.15277 ---
all0.15475 29707 --
obs0.15475 28131 96.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.478 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.127 Å0.142 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3131 0 33 428 3592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213260
X-RAY DIFFRACTIONr_bond_other_d0.0030.023065
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.9554437
X-RAY DIFFRACTIONr_angle_other_deg0.82736949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6135403
X-RAY DIFFRACTIONr_chiral_restr0.0710.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023700
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02727
X-RAY DIFFRACTIONr_nbd_refined0.1980.2724
X-RAY DIFFRACTIONr_nbd_other0.2290.23690
X-RAY DIFFRACTIONr_nbtor_other0.0940.21935
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2294
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.2168
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.240
X-RAY DIFFRACTIONr_mcbond_it0.4681.52011
X-RAY DIFFRACTIONr_mcangle_it0.88623239
X-RAY DIFFRACTIONr_scbond_it1.51331249
X-RAY DIFFRACTIONr_scangle_it2.5694.51198
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 98 -
Rwork0.377 2078 -
obs-2078 92.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8057-0.41850.11041.78240.82121.90490.12570.1676-0.0624-0.2583-0.21630.12490.1046-0.04580.09050.2070.0829-0.02620.0858-0.03950.09557.70339.17623.36
20.424-0.0503-0.0111.72071.091.27050.0679-0.0214-0.0580.275-0.0842-0.0030.29750.03340.01630.20760.0033-0.00740.08060.01260.098512.54648.50949.101
31.92580.07580.70286.38653.04534.25560.1064-0.2038-0.08540.88470.2553-0.77780.55780.257-0.36170.21880.0574-0.18980.1338-0.01260.190128.46452.76959.404
40.90540.3630.37643.42181.47912.35940.11150.1386-0.1098-0.25020.2617-1.09010.11820.5838-0.37320.07710.08910.05830.1907-0.08340.422834.6444.50437.54
5-8.838512.587712.681817.9965-36.545578.46340.06110.96311.2282-0.93610.68410.6392-1.8764-1.4734-0.74520.0034-0.0015-0.00220.0057-0.00080.002818.43156.03929.382
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 352 - 35
2X-RAY DIFFRACTION1AA299 - 405299 - 405
3X-RAY DIFFRACTION2AA36 - 9636 - 96
4X-RAY DIFFRACTION2AA205 - 241205 - 241
5X-RAY DIFFRACTION2AA282 - 298282 - 298
6X-RAY DIFFRACTION3AA242 - 281242 - 281
7X-RAY DIFFRACTION4AA97 - 20497 - 204
8X-RAY DIFFRACTION5AD7011
Refinement
*PLUS
Lowest resolution: 58.7 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.192 / Rfactor Rwork: 0.155
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.186
LS refinement shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.9 Å

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