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- PDB-4tlx: Kutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADred-NADP+-L-orn -

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Basic information

Entry
Database: PDB / ID: 4tlx
TitleKutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADred-NADP+-L-orn
ComponentsKtzI
KeywordsOXIDOREDUCTASE / hydroxylase / flavin / ornithine / monooxygenase
Function / homology
Function and homology information


L-lysine N6-monooxygenase (NADPH) / L-lysine 6-monooxygenase (NADPH) activity / biosynthetic process / nucleotide binding
Similarity search - Function
L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L-ornithine / L-lysine N6-monooxygenase MbtG
Similarity search - Component
Biological speciesKutzneria sp. 744 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsSetser, J.W. / Drennan, C.L.
CitationJournal: Biochemistry / Year: 2014
Title: Crystallographic Evidence of Drastic Conformational Changes in the Active Site of a Flavin-Dependent N-Hydroxylase.
Authors: Setser, J.W. / Heemstra, J.R. / Walsh, C.T. / Drennan, C.L.
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KtzI
B: KtzI
C: KtzI
D: KtzI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,70825
Polymers197,7044
Non-polymers7,00421
Water10,611589
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27890 Å2
ΔGint-147 kcal/mol
Surface area58010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.150, 156.906, 163.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
KtzI / Peptide monooxygenase


Mass: 49425.938 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kutzneria sp. 744 (bacteria) / Gene: ktzI, KUTG_08917 / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A8CF85

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Non-polymers , 5 types, 610 molecules

#2: Chemical
ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-ORN / L-ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12N2O2
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.9-1.15 M potassium thiocyanate, 22-25% PEG 3350, 0.1 M Bis-tris propane pH 8.5
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.23→66 Å / Num. obs: 106307 / % possible obs: 99 % / Redundancy: 4.2 % / Rsym value: 0.065 / Net I/σ(I): 20.5
Reflection shellResolution: 2.23→2.27 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.572 / % possible all: 98.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S5W

3s5w


Resolution: 2.23→49.819 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 4888 4.94 %
Rwork0.1865 --
obs0.1879 98964 92.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.23→49.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12824 0 449 589 13862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113614
X-RAY DIFFRACTIONf_angle_d1.20518625
X-RAY DIFFRACTIONf_dihedral_angle_d16.0274731
X-RAY DIFFRACTIONf_chiral_restr0.0992052
X-RAY DIFFRACTIONf_plane_restr0.0052409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.25090.2961770.241589X-RAY DIFFRACTION48
2.2509-2.27740.2762920.2461961X-RAY DIFFRACTION57
2.2774-2.30510.2791290.2462169X-RAY DIFFRACTION66
2.3051-2.33430.27991440.24232576X-RAY DIFFRACTION77
2.3343-2.3650.30971260.2432809X-RAY DIFFRACTION84
2.365-2.39740.33281580.24193004X-RAY DIFFRACTION89
2.3974-2.43170.3011390.23783080X-RAY DIFFRACTION92
2.4317-2.4680.26471380.23153122X-RAY DIFFRACTION92
2.468-2.50650.25081600.23353024X-RAY DIFFRACTION91
2.5065-2.54760.25861670.22833384X-RAY DIFFRACTION99
2.5476-2.59150.26661910.21643271X-RAY DIFFRACTION99
2.5915-2.63870.26011650.22283356X-RAY DIFFRACTION99
2.6387-2.68940.25771820.21673305X-RAY DIFFRACTION99
2.6894-2.74430.23211490.21693368X-RAY DIFFRACTION100
2.7443-2.8040.24311800.21553360X-RAY DIFFRACTION100
2.804-2.86920.24871750.2113324X-RAY DIFFRACTION99
2.8692-2.94090.23121800.21543337X-RAY DIFFRACTION99
2.9409-3.02040.24161740.21333387X-RAY DIFFRACTION100
3.0204-3.10930.24371950.22683326X-RAY DIFFRACTION99
3.1093-3.20970.24811750.21613280X-RAY DIFFRACTION98
3.2097-3.32440.24611640.19853275X-RAY DIFFRACTION97
3.3244-3.45740.20631810.18243373X-RAY DIFFRACTION100
3.4574-3.61470.21551930.17213365X-RAY DIFFRACTION100
3.6147-3.80520.17922130.16743369X-RAY DIFFRACTION100
3.8052-4.04360.18421800.16133408X-RAY DIFFRACTION100
4.0436-4.35560.16591640.13923417X-RAY DIFFRACTION100
4.3556-4.79360.13891670.143333X-RAY DIFFRACTION97
4.7936-5.48650.16991850.14153440X-RAY DIFFRACTION100
5.4865-6.90950.18651730.1673508X-RAY DIFFRACTION100
6.9095-49.83170.17641720.15623556X-RAY DIFFRACTION97

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