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- PDB-4co9: Crystal structure of kynurenine formamidase from Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 4co9
TitleCrystal structure of kynurenine formamidase from Bacillus anthracis
ComponentsKYNURENINE FORMAMIDASE
KeywordsHYDROLASE / AEROBIC TRYPTOPHAN DEGRADATION VIA ANTHRANILATE.
Function / homology
Function and homology information


arylformamidase / formamidase activity / arylformamidase activity / anthranilate metabolic process / tryptophan catabolic process to kynurenine / zinc ion binding
Similarity search - Function
Kynurenine formamidase, bacteria / Putative cyclase / Kynurenine formamidase/cyclase-like / Kynurenine formamidase superfamily / Putative cyclase / Glucose Oxidase; domain 1 / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / ethanedial / Kynurenine formamidase
Similarity search - Component
Biological speciesBACILLUS ANTHRACIS (anthrax bacterium)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDiaz-Saez, L. / Srikannathasan, V. / Zoltner, M. / Hunter, W.N.
CitationJournal: Biochem.J. / Year: 2014
Title: Structure of Bacterial Kynurenine Formamidase Reveals a Crowded Binuclear-Zinc Catalytic Site Primed to Generate a Potent Nucleophile.
Authors: Diaz-Saez, L. / Srikannathasan, V. / Zoltner, M. / Hunter, W.N.
History
DepositionJan 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other
Revision 1.2Sep 3, 2014Group: Database references
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KYNURENINE FORMAMIDASE
B: KYNURENINE FORMAMIDASE
C: KYNURENINE FORMAMIDASE
D: KYNURENINE FORMAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,65322
Polymers93,6584
Non-polymers99518
Water16,322906
1
C: KYNURENINE FORMAMIDASE
D: KYNURENINE FORMAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,28610
Polymers46,8292
Non-polymers4568
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-192.2 kcal/mol
Surface area16360 Å2
MethodPISA
2
A: KYNURENINE FORMAMIDASE
B: KYNURENINE FORMAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,36812
Polymers46,8292
Non-polymers53910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-187.5 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.710, 66.020, 83.760
Angle α, β, γ (deg.)90.00, 90.32, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 209
2010B3 - 209
1020A4 - 208
2020C4 - 208
1030A4 - 208
2030D4 - 208
1040B4 - 208
2040C4 - 208
1050B4 - 208
2050D4 - 208
1060C4 - 209
2060D4 - 209

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
KYNURENINE FORMAMIDASE / KFA / KFASE / ARYLFORMAMIDASE / N-FORMYLKYNURENINE FORMAMIDASE / FKF


Mass: 23414.561 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Strain: AMES / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81PP9, arylformamidase

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Non-polymers , 5 types, 924 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#5: Chemical ChemComp-GXT / ethanedial / Glyoxal


Mass: 58.036 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 906 / 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: 2.22 Å3/Da / Density % sol: 44.06 % / Description: NONE
Crystal growTemperature: 293 K
Details: 100 MM TRIS-HCL PH 8.5, 150 MM MGCL2, 30 % (W/V) PEG 4000 AND 1.5 % (V/V) DIOXANE. 293 K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Jul 27, 2013 / Details: MIRRORS
RadiationMonochromator: SI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→42.48 Å / Num. obs: 202165 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.1
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 4.3 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: KYNURENINE FORMAMIDASE FROM BURKHOLDERIA CENOCEPACIA. TO BE SUBMITED

Resolution: 1.95→83.76 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.595 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20663 2954 5.1 %RANDOM
Rwork0.17145 ---
obs0.17323 55358 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.886 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.17 Å2
2--0.37 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.95→83.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6473 0 37 906 7416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196835
X-RAY DIFFRACTIONr_bond_other_d0.0060.026668
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9719300
X-RAY DIFFRACTIONr_angle_other_deg1.2513.00315473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3145822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.39624.888313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.896151210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2771532
X-RAY DIFFRACTIONr_chiral_restr0.0740.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217480
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021416
X-RAY DIFFRACTIONr_nbd_refined0.2540.22478
X-RAY DIFFRACTIONr_nbd_other0.1920.26712
X-RAY DIFFRACTIONr_nbtor_refined0.1750.23276
X-RAY DIFFRACTIONr_nbtor_other0.0850.23157
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2231
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1350.26
X-RAY DIFFRACTIONr_metal_ion_refined0.620.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.298
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.212
X-RAY DIFFRACTIONr_symmetry_hbond_other0.2670.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9021.4413299
X-RAY DIFFRACTIONr_mcbond_other0.9021.4413298
X-RAY DIFFRACTIONr_mcangle_it1.5582.1564117
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9731.6023536
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6342.3365183
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A128510.1
12B128510.1
21A131270.07
22C131270.07
31A126340.11
32D126340.11
41B128410.09
42C128410.09
51B130810.07
52D130810.07
61C128260.1
62D128260.1
LS refinement shellResolution: 1.952→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 205 -
Rwork0.211 3902 -
obs--94.81 %

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