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- PDB-4e15: Crystal structure of kynurenine formamidase conjugated with an in... -

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Basic information

Entry
Database: PDB / ID: 4.0E+15
TitleCrystal structure of kynurenine formamidase conjugated with an inhibitor
Componentskynurenine formamidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / alpha/beta hydrolase fold / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


arylformamidase / arylformamidase activity / lipase activity / tryptophan catabolic process to kynurenine
Similarity search - Function
Kynurenine formamidase, vertebrates/fungi-type / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Kynurenine formamidase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHan, Q. / Robinson, H. / Li, J.
CitationJournal: Biochem.J. / Year: 2012
Title: Biochemical identification and crystal structure of kynurenine formamidase from Drosophila melanogaster.
Authors: Han, Q. / Robinson, H. / Li, J.
History
DepositionMar 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / 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_ref_seq_dif.details / _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: kynurenine formamidase
B: kynurenine formamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0557
Polymers70,7442
Non-polymers3105
Water9,278515
1
A: kynurenine formamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6205
Polymers35,3721
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: kynurenine formamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4342
Polymers35,3721
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.602, 76.021, 210.377
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein kynurenine formamidase / arylformamidase / aryl-formylamine amidohydrolase / formylkynureninase / CG9542 / RH42281p


Mass: 35372.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG9542, Dmel_CG9542 / Plasmid: PTYB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9VMC9, arylformamidase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.02 Å3/Da / Density % sol: 39.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 18% PEG4000, 8% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 91964 / Num. obs: 90494 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 25
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4 / Num. unique all: 7888

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E11

4e11


Resolution: 1.5→46.7 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19808 4501 5 %RANDOM
Rwork0.17096 ---
obs0.17235 85145 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.872 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4967 0 20 515 5502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0225108
X-RAY DIFFRACTIONr_angle_refined_deg2.071.9416920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1695603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.59323.514259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63215856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2021536
X-RAY DIFFRACTIONr_chiral_restr0.140.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213902
X-RAY DIFFRACTIONr_mcbond_it1.2891.53013
X-RAY DIFFRACTIONr_mcangle_it2.08624896
X-RAY DIFFRACTIONr_scbond_it3.40832095
X-RAY DIFFRACTIONr_scangle_it5.1284.52024
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 307 -
Rwork0.209 5374 -
obs--84.28 %

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