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- PDB-4e11: Crystal structure of kynurenine formamidase from Drosophila melan... -

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Basic information

Entry
Database: PDB / ID: 400000000000
TitleCrystal structure of kynurenine formamidase from Drosophila melanogaster
Componentskynurenine formamidase
KeywordsHYDROLASE / alpha/beta hydrolase fold
Function / homology
Function and homology information


arylformamidase / arylformamidase activity / L-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
BETA-MERCAPTOETHANOL / Kynurenine formamidase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 / pdbx_struct_special_symmetry / 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5677
Polymers35,2181
Non-polymers3496
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.771, 47.085, 85.683
Angle α, β, γ (deg.)90.00, 90.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-405-

NA

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Components

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


Mass: 35217.914 Da / Num. of mol.: 1
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-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% ethylene glycol, 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: Apr 8, 2011
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: 2→50 Å / Num. all: 20558 / Num. obs: 19948 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 23.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.62 / Num. unique all: 1994

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PBL

2pbl


Resolution: 2→42.84 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 16.669 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27344 1015 5.1 %RANDOM
Rwork0.22493 ---
obs0.22743 18772 95.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.526 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.05 Å2
2---0.01 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 21 83 2564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222563
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.9363469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7445305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50323.538130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.83315432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.311518
X-RAY DIFFRACTIONr_chiral_restr0.1130.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211960
X-RAY DIFFRACTIONr_mcbond_it0.7471.51513
X-RAY DIFFRACTIONr_mcangle_it1.20122465
X-RAY DIFFRACTIONr_scbond_it2.34431050
X-RAY DIFFRACTIONr_scangle_it3.114.51004
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 67 -
Rwork0.321 1346 -
obs--92.66 %
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)
13.04691.06980.87214.43860.31761.30340.098-0.8847-0.63491.55690.26110.1852-0.4978-0.4589-0.35911.0468-0.01730.22231.1578-0.02750.467119.86998.460134.2363
21.87040.36220.64973.6937-0.20251.24840.1787-0.2947-0.06310.2155-0.22840.0390.1128-0.31370.04970.0658-0.0777-0.00030.13060.01610.119623.5880.52428.7931
31.8114-0.10010.35921.81130.4041.58430.2149-0.6097-0.13560.5032-0.2623-0.09690.221-0.25380.04740.3295-0.2258-0.03190.41450.08940.16128.3286-3.300724.4762
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 36
2X-RAY DIFFRACTION2A37 - 186
3X-RAY DIFFRACTION3A187 - 299

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