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- PDB-4tm1: Kutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADred-NADP+-Br -

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Basic information

Entry
Database: PDB / ID: 4tm1
TitleKutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADred-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 / 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: 2.39 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 / 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)206,62447
Polymers197,7044
Non-polymers8,92143
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32590 Å2
ΔGint-158 kcal/mol
Surface area57260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.888, 151.711, 162.388
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 / Production host: Escherichia coli (E. coli) / 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


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


Mass: 79.904 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.2-1.4 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: Apr 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 78161 / % possible obs: 96.8 % / Redundancy: 5.5 % / Rsym value: 0.107 / Net I/σ(I): 14.7
Reflection shellResolution: 2.39→2.43 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.569 / % possible all: 98.1

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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: 2.39→45.902 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2222 3955 5.06 %
Rwork0.1989 --
obs0.2001 78126 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→45.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12752 0 439 427 13618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913508
X-RAY DIFFRACTIONf_angle_d1.28918492
X-RAY DIFFRACTIONf_dihedral_angle_d16.8714684
X-RAY DIFFRACTIONf_chiral_restr0.1592044
X-RAY DIFFRACTIONf_plane_restr0.0052388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.41860.31481280.26352522X-RAY DIFFRACTION93
2.4186-2.44920.27091340.25472631X-RAY DIFFRACTION98
2.4492-2.48140.30841340.23742673X-RAY DIFFRACTION98
2.4814-2.51540.28161560.23852609X-RAY DIFFRACTION98
2.5154-2.55130.29431460.23782670X-RAY DIFFRACTION98
2.5513-2.58940.25571510.23312619X-RAY DIFFRACTION98
2.5894-2.62990.28971410.2312702X-RAY DIFFRACTION98
2.6299-2.6730.25011420.2382614X-RAY DIFFRACTION97
2.673-2.71910.27831390.24222629X-RAY DIFFRACTION97
2.7191-2.76850.3171530.24072577X-RAY DIFFRACTION96
2.7685-2.82170.25631430.22972438X-RAY DIFFRACTION89
2.8217-2.87930.27581430.23062587X-RAY DIFFRACTION97
2.8793-2.94190.2561330.23472692X-RAY DIFFRACTION98
2.9419-3.01030.27091300.24382681X-RAY DIFFRACTION98
3.0103-3.08560.28881120.24022707X-RAY DIFFRACTION99
3.0856-3.1690.31561430.23982686X-RAY DIFFRACTION98
3.169-3.26220.25421270.22592671X-RAY DIFFRACTION98
3.2622-3.36750.21931660.21572649X-RAY DIFFRACTION98
3.3675-3.48780.22481500.19632649X-RAY DIFFRACTION97
3.4878-3.62740.23331310.19232603X-RAY DIFFRACTION95
3.6274-3.79240.19611460.18532469X-RAY DIFFRACTION90
3.7924-3.99230.19041570.17722705X-RAY DIFFRACTION99
3.9923-4.24220.18231440.16442732X-RAY DIFFRACTION99
4.2422-4.56950.19011300.16322737X-RAY DIFFRACTION98
4.5695-5.02890.16681210.1512724X-RAY DIFFRACTION98
5.0289-5.75530.18061400.16752570X-RAY DIFFRACTION92
5.7553-7.24650.20551460.19442821X-RAY DIFFRACTION99
7.2465-45.91060.15761690.16542804X-RAY DIFFRACTION95

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