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- PDB-4tm3: Kutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADox-Br -

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Basic information

Entry
Database: PDB / ID: 4tm3
TitleKutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADox-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 / FLAVIN-ADENINE DINUCLEOTIDE / L-lysine N6-monooxygenase MbtG
Similarity search - Component
Biological speciesKutzneria sp. 744 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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)204,52254
Polymers197,7044
Non-polymers6,81850
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28890 Å2
ΔGint-138 kcal/mol
Surface area57880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.814, 151.943, 161.870
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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical...
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.48 Å3/Da / Density % sol: 50.45 %
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: Apr 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 117046 / % possible obs: 99.5 % / Redundancy: 5.2 % / Rsym value: 0.089 / Net I/σ(I): 16.5
Reflection shellResolution: 2.09→2.13 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.537 / % possible all: 99.9

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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: 2.09→45.506 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2365 5814 5 %
Rwork0.2051 --
obs0.2067 116327 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→45.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12734 0 258 465 13457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01513282
X-RAY DIFFRACTIONf_angle_d1.65718150
X-RAY DIFFRACTIONf_dihedral_angle_d13.6844610
X-RAY DIFFRACTIONf_chiral_restr0.272008
X-RAY DIFFRACTIONf_plane_restr0.0062372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.11280.3091790.25993442X-RAY DIFFRACTION94
2.1128-2.13770.27871930.25143654X-RAY DIFFRACTION100
2.1377-2.16370.29481770.2483697X-RAY DIFFRACTION100
2.1637-2.19110.27951900.24583615X-RAY DIFFRACTION100
2.1911-2.220.27661950.23483705X-RAY DIFFRACTION100
2.22-2.25040.32221720.26383611X-RAY DIFFRACTION98
2.2504-2.28250.30171860.25363657X-RAY DIFFRACTION99
2.2825-2.31660.27681830.23253648X-RAY DIFFRACTION99
2.3166-2.35280.27331990.24153656X-RAY DIFFRACTION100
2.3528-2.39140.31061910.23573645X-RAY DIFFRACTION100
2.3914-2.43260.25131960.23753681X-RAY DIFFRACTION100
2.4326-2.47680.30332020.23673664X-RAY DIFFRACTION100
2.4768-2.52450.30791980.24313667X-RAY DIFFRACTION100
2.5245-2.5760.29681880.243721X-RAY DIFFRACTION100
2.576-2.6320.27791870.23973617X-RAY DIFFRACTION100
2.632-2.69320.28681840.23683675X-RAY DIFFRACTION99
2.6932-2.76060.27661890.25233691X-RAY DIFFRACTION100
2.7606-2.83520.28262010.2383653X-RAY DIFFRACTION99
2.8352-2.91860.30622000.23463673X-RAY DIFFRACTION100
2.9186-3.01280.26071970.24223711X-RAY DIFFRACTION100
3.0128-3.12040.28312010.24633695X-RAY DIFFRACTION100
3.1204-3.24530.24082160.23093687X-RAY DIFFRACTION100
3.2453-3.3930.23031990.21213688X-RAY DIFFRACTION100
3.393-3.57180.22572010.20273678X-RAY DIFFRACTION99
3.5718-3.79550.23281960.19063721X-RAY DIFFRACTION99
3.7955-4.08840.17121980.1763711X-RAY DIFFRACTION100
4.0884-4.49950.18062030.15433745X-RAY DIFFRACTION100
4.4995-5.14980.18281900.15253759X-RAY DIFFRACTION99
5.1498-6.48520.22091920.18343791X-RAY DIFFRACTION99
6.4852-45.51710.18362110.16743955X-RAY DIFFRACTION99

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