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- PDB-4cob: Crystal structure kynurenine formamidase from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4cob
TitleCrystal structure kynurenine formamidase from Pseudomonas aeruginosa
ComponentsKYNURENINE FORMAMIDASE
KeywordsHYDROLASE / AEROBIC TRYPTOPHAN DEGRADATION VIA ANTHRANILATE
Function / homology
Function and homology information


arylformamidase / formamidase activity / arylformamidase activity / anthranilate metabolic process / L-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
Kynurenine formamidase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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 28, 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 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)46,9796
Polymers46,7172
Non-polymers2624
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-187.4 kcal/mol
Surface area16550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.721, 112.721, 90.761
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 23358.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9I234, arylformamidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.41 Å3/Da / Density % sol: 49.04 % / Description: NONE
Crystal growTemperature: 293 K
Details: 0.1 M HEPES PH 7.5, 20 % (W/V) PEG [POLY(ETHYLENE GLYCOL)] 4000, AND 10 % (V/V) 2-PROPANOL. 293 K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.37→28.9 Å / Num. obs: 27365 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.8
Reflection shellResolution: 2.37→2.46 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.4 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R61

1r61


Resolution: 2.37→97.62 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.732 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19367 1377 5 %RANDOM
Rwork0.15047 ---
obs0.15265 25966 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.986 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20.56 Å20 Å2
2--1.11 Å20 Å2
3----3.6 Å2
Refinement stepCycle: LAST / Resolution: 2.37→97.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3158 0 4 187 3349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193307
X-RAY DIFFRACTIONr_bond_other_d0.0010.023136
X-RAY DIFFRACTIONr_angle_refined_deg1.8931.9724552
X-RAY DIFFRACTIONr_angle_other_deg0.89837230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8945418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18422.867143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14715478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7971529
X-RAY DIFFRACTIONr_chiral_restr0.1030.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213757
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02728
X-RAY DIFFRACTIONr_nbd_refined0.2540.2759
X-RAY DIFFRACTIONr_nbd_other0.1980.23061
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21611
X-RAY DIFFRACTIONr_nbtor_other0.0930.21876
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.270
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0160.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3830.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.30.22
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0860.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7574.7921666
X-RAY DIFFRACTIONr_mcbond_other3.7494.791665
X-RAY DIFFRACTIONr_mcangle_it5.2287.1712086
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.4225.3921641
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.7347.8692466
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
LS refinement shellResolution: 2.366→2.427 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 94 -
Rwork0.294 1751 -
obs--91.97 %

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