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

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Basic information

Entry
Database: PDB / ID: 4tlz
TitleKutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADox-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 / 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: 2.411 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)204,66124
Polymers197,7044
Non-polymers6,95720
Water10,557586
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28180 Å2
ΔGint-146 kcal/mol
Surface area58300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.620, 157.660, 165.293
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, 606 molecules

#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-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.: 8 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / 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: 2.79 Å3/Da / Density % sol: 55.89 %
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, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.41→100 Å / Num. obs: 83380 / % possible obs: 99 % / Redundancy: 4.1 % / Net I/σ(I): 21.3
Reflection shellResolution: 2.41→2.45 Å / % possible obs: 99.5 % / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.568

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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: 2.411→47.299 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2148 4110 5.05 %
Rwork0.1784 --
obs0.1802 81405 94.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.411→47.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12871 0 448 586 13905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01213662
X-RAY DIFFRACTIONf_angle_d1.4118683
X-RAY DIFFRACTIONf_dihedral_angle_d18.0464767
X-RAY DIFFRACTIONf_chiral_restr0.2662052
X-RAY DIFFRACTIONf_plane_restr0.0052418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.411-2.43890.272790.22851675X-RAY DIFFRACTION60
2.4389-2.46870.25221090.20932008X-RAY DIFFRACTION73
2.4687-2.49990.27361200.21162154X-RAY DIFFRACTION78
2.4999-2.53280.271270.21912382X-RAY DIFFRACTION85
2.5328-2.56750.28911360.22722467X-RAY DIFFRACTION88
2.5675-2.60420.24971270.22162577X-RAY DIFFRACTION94
2.6042-2.6430.28011250.22272658X-RAY DIFFRACTION94
2.643-2.68430.27161490.21792672X-RAY DIFFRACTION96
2.6843-2.72830.27981520.22062678X-RAY DIFFRACTION97
2.7283-2.77540.25161420.2052736X-RAY DIFFRACTION99
2.7754-2.82580.26941270.2012814X-RAY DIFFRACTION99
2.8258-2.88020.2341390.19992741X-RAY DIFFRACTION99
2.8802-2.9390.23111570.20162804X-RAY DIFFRACTION99
2.939-3.00290.24891550.20272766X-RAY DIFFRACTION99
3.0029-3.07270.28151550.20562760X-RAY DIFFRACTION100
3.0727-3.14950.2511710.21472773X-RAY DIFFRACTION99
3.1495-3.23470.26431430.21312775X-RAY DIFFRACTION99
3.2347-3.32980.24211510.19922744X-RAY DIFFRACTION98
3.3298-3.43730.27651370.19372817X-RAY DIFFRACTION99
3.4373-3.56010.23411650.18572782X-RAY DIFFRACTION99
3.5601-3.70260.22161360.17662797X-RAY DIFFRACTION99
3.7026-3.8710.2011490.16892822X-RAY DIFFRACTION100
3.871-4.0750.19391520.1582786X-RAY DIFFRACTION99
4.075-4.33010.15431400.13542796X-RAY DIFFRACTION98
4.3301-4.66420.14761580.13392814X-RAY DIFFRACTION99
4.6642-5.13310.14551520.12482837X-RAY DIFFRACTION100
5.1331-5.87460.18691430.14582847X-RAY DIFFRACTION99
5.8746-7.39690.1851560.17142881X-RAY DIFFRACTION99
7.3969-47.30850.14771580.15312932X-RAY DIFFRACTION96

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