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- PDB-4tm0: Kutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADred-ox-NADP+-L-orn -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4tm0
TitleKutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADred-ox-NADP+-L-orn
ComponentsKtzI
KeywordsOXIDOREDUCTASE / hydroxylase / flavin / monooxygenase / ornithine
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
FLAVIN-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: 2.74 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_conn_angle / 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)204,66124
Polymers197,7044
Non-polymers6,95720
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29420 Å2
ΔGint-143 kcal/mol
Surface area58040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.029, 156.401, 164.496
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, 259 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#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-ORN / L-ornithine / 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.: 8 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.77 Å3/Da / Density % sol: 55.54 %
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: Feb 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.74→100 Å / Num. obs: 57847 / % possible obs: 97.9 % / Redundancy: 4.5 % / Net I/σ(I): 21.3
Reflection shellResolution: 2.74→2.79 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.567 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S5W
Resolution: 2.74→47.158 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 2744 5.08 %
Rwork0.1865 --
obs0.188 54045 91.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.74→47.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12774 0 448 239 13461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01413565
X-RAY DIFFRACTIONf_angle_d1.51818562
X-RAY DIFFRACTIONf_dihedral_angle_d18.6664698
X-RAY DIFFRACTIONf_chiral_restr0.2132050
X-RAY DIFFRACTIONf_plane_restr0.0082396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.77480.3158670.24781219X-RAY DIFFRACTION44
2.7748-2.82520.29871090.23471664X-RAY DIFFRACTION60
2.8252-2.87950.30181120.24332116X-RAY DIFFRACTION77
2.8795-2.93830.32321250.24172407X-RAY DIFFRACTION86
2.9383-3.00220.30071330.23782574X-RAY DIFFRACTION93
3.0022-3.0720.25911460.24172685X-RAY DIFFRACTION96
3.072-3.14880.28311540.23922720X-RAY DIFFRACTION98
3.1488-3.23390.26851420.22782736X-RAY DIFFRACTION98
3.2339-3.32910.22091540.2092717X-RAY DIFFRACTION98
3.3291-3.43650.21671350.19692696X-RAY DIFFRACTION96
3.4365-3.55930.24541500.19112759X-RAY DIFFRACTION98
3.5593-3.70170.20421380.18092762X-RAY DIFFRACTION99
3.7017-3.87010.22521430.17122767X-RAY DIFFRACTION99
3.8701-4.07410.19671530.16742769X-RAY DIFFRACTION99
4.0741-4.32920.18281410.1492771X-RAY DIFFRACTION98
4.3292-4.66310.18911470.14732685X-RAY DIFFRACTION95
4.6631-5.13190.15261530.13622814X-RAY DIFFRACTION99
5.1319-5.87330.19741430.16942801X-RAY DIFFRACTION98
5.8733-7.39510.20941490.19632756X-RAY DIFFRACTION95
7.3951-47.16510.17211500.18982883X-RAY DIFFRACTION95

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