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- PDB-4cz1: Crystal structure of kynurenine formamidase from Bacillus anthrac... -

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Basic information

Entry
Database: PDB / ID: 4cz1
TitleCrystal structure of kynurenine formamidase from Bacillus anthracis complexed with 2-aminoacetophenone.
ComponentsKYNURENINE FORMAMIDASE
KeywordsHYDROLASE / TRYPTOPHAN DEGRADATION PATHWAY 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
2-aminoacetophenone / Kynurenine formamidase
Similarity search - Component
Biological speciesBACILLUS ANTHRACIS STR. AMES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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
DepositionApr 16, 2014Deposition site: PDBE / Processing site: PDBE
SupersessionApr 30, 2014ID: 4COA
Revision 1.0Apr 30, 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_ncs_dom_lim / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

Downloads & links

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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)93,60916
Polymers92,8774
Non-polymers73112
Water7,422412
1
A: KYNURENINE FORMAMIDASE
B: KYNURENINE FORMAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8608
Polymers46,4392
Non-polymers4216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-195.7 kcal/mol
Surface area16470 Å2
MethodPISA
2
C: KYNURENINE FORMAMIDASE
D: KYNURENINE FORMAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7498
Polymers46,4392
Non-polymers3106
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-191.1 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.695, 66.561, 84.061
Angle α, β, γ (deg.)90.00, 90.24, 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:

Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA4 - 2084 - 208
21PROPROBB4 - 2084 - 208
12PROPROAA4 - 2084 - 208
22PROPROCC4 - 2084 - 208
13PROPROAA4 - 2084 - 208
23PROPRODD4 - 2084 - 208
14ILEILEBB4 - 2094 - 209
24ILEILECC4 - 2094 - 209
15ILEILEBB4 - 2094 - 209
25ILEILEDD4 - 2094 - 209
16ILEILECC4 - 2094 - 209
26ILEILEDD4 - 2094 - 209

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 23219.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS ANTHRACIS STR. AMES (bacteria)
Gene: KYNB / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81PP9, arylformamidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-VNJ / 2-aminoacetophenone


Mass: 135.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsZINC ION (ZN): ZN2+ BINDING ACTIVE SITE RESIDUES 2-AMINOACETOPHENONE (2AT): PLACE AT THE ACTIVE SITE

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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: 2.23 Å3/Da / Density % sol: 44.88 % / Description: NONE
Crystal growTemperature: 293 K
Details: 100 MM TRIS-HCL PH 8.5, 140 MM MGCL2 AND 30 % (W/V) PEG 4000. 293 K. PROTEIN WAS PREVIOUSLY INCUBATED WITH 5 % (V/V) 2-AMINOACETOPHENONE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9791
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.842
11-h,-k,l20.158
ReflectionResolution: 2.25→42.64 Å / Num. obs: 38046 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.8
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.2 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CO9

4co9


Resolution: 2.24→42.64 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.898 / SU B: 4.232 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 1916 5 %RANDOM
Rwork0.1837 ---
obs0.18576 36106 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.693 Å2
Baniso -1Baniso -2Baniso -3
1-7.17 Å20 Å26.27 Å2
2--5.74 Å20 Å2
3----12.91 Å2
Refinement stepCycle: LAST / Resolution: 2.24→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6467 0 21 412 6900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196677
X-RAY DIFFRACTIONr_bond_other_d0.0090.026443
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.9699098
X-RAY DIFFRACTIONr_angle_other_deg1.3433.00114909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7275821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66824.933300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.365151134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6571528
X-RAY DIFFRACTIONr_chiral_restr0.10.21049
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217431
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021405
X-RAY DIFFRACTIONr_nbd_refined0.2380.21618
X-RAY DIFFRACTIONr_nbd_other0.1970.26205
X-RAY DIFFRACTIONr_nbtor_refined0.1760.23221
X-RAY DIFFRACTIONr_nbtor_other0.0880.23373
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2163
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1320.26
X-RAY DIFFRACTIONr_metal_ion_refined0.2050.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3120.245
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5090.22
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1450.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0081.9143296
X-RAY DIFFRACTIONr_mcbond_other2.0061.9143295
X-RAY DIFFRACTIONr_mcangle_it3.092.8634113
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4952.1893381
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9633.1644985
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)
11A126070.07
12B126070.07
21A128010.05
22C128010.05
31A124470.09
32D124470.09
41B127570.07
42C127570.07
51B128100.06
52D128100.06
61C125620.09
62D125620.09
LS refinement shellResolution: 2.241→2.299 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 147 -
Rwork0.22 2226 -
obs--82.57 %

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