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- PDB-4tm4: Kutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADox-red-NADP+-Br -

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Basic information

Entry
Database: PDB / ID: 4tm4
TitleKutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADox-red-NADP+-Br
ComponentsKtzI
KeywordsOXIDOREDUCTASE / hydroxylase / flavin / ornithine / monooxygenase
Function / homology
Function and homology information


L-lysine N6-monooxygenase (NADPH) / L-lysine 6-monooxygenase (NADPH) activity / cellular biosynthetic process / organonitrogen compound 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
BROMIDE ION / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L-lysine N6-monooxygenase MbtG
Similarity search - Component
Biological speciesKutzneria sp. 744 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.632 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 1.1Sep 24, 2014Group: Structure summary
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
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_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords
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_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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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)206,30543
Polymers197,7044
Non-polymers8,60139
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32050 Å2
ΔGint-158 kcal/mol
Surface area58190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.387, 151.956, 163.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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): BL21f / References: UniProt: A8CF85
#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 / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical...
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.9-1.2 M sodium bromide, 22-25% PEG 3350, 0.1 M Bis-tris propane pH 7.5
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: Dec 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. obs: 61333 / % possible obs: 99.2 % / Redundancy: 4.9 % / Rsym value: 0.097 / Net I/σ(I): 14.8
Reflection shellResolution: 2.63→2.68 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.533 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S5W

3s5w


Resolution: 2.632→46.122 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 3067 5.03 %
Rwork0.1929 --
obs0.1945 60995 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.632→46.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12725 0 435 258 13418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01513479
X-RAY DIFFRACTIONf_angle_d1.62218456
X-RAY DIFFRACTIONf_dihedral_angle_d17.0494664
X-RAY DIFFRACTIONf_chiral_restr0.1452044
X-RAY DIFFRACTIONf_plane_restr0.0082383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.632-2.6730.36241250.28292484X-RAY DIFFRACTION94
2.673-2.71680.33091450.25922492X-RAY DIFFRACTION96
2.7168-2.76360.28341380.25042646X-RAY DIFFRACTION99
2.7636-2.81390.32531490.23582575X-RAY DIFFRACTION100
2.8139-2.8680.28991630.23582602X-RAY DIFFRACTION99
2.868-2.92650.22021270.22792632X-RAY DIFFRACTION99
2.9265-2.99010.26991250.24012626X-RAY DIFFRACTION100
2.9901-3.05970.27511320.24462652X-RAY DIFFRACTION100
3.0597-3.13620.29291160.23682626X-RAY DIFFRACTION100
3.1362-3.22090.30441260.2222645X-RAY DIFFRACTION100
3.2209-3.31570.27111460.20892610X-RAY DIFFRACTION98
3.3157-3.42270.23391610.19782565X-RAY DIFFRACTION99
3.4227-3.5450.20991400.18582645X-RAY DIFFRACTION100
3.545-3.68690.22061340.18352633X-RAY DIFFRACTION100
3.6869-3.85460.18761550.17672657X-RAY DIFFRACTION100
3.8546-4.05770.19851560.16882632X-RAY DIFFRACTION100
4.0577-4.31170.20181400.16222682X-RAY DIFFRACTION100
4.3117-4.64440.16021080.15782634X-RAY DIFFRACTION98
4.6444-5.11120.16881230.15512725X-RAY DIFFRACTION100
5.1112-5.84950.19691560.17552686X-RAY DIFFRACTION100
5.8495-7.36490.21181390.19552675X-RAY DIFFRACTION98
7.3649-46.12890.21011630.18562804X-RAY DIFFRACTION98

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