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- PDB-4d7e: An unprecedented NADPH domain conformation in Lysine Monooxygenas... -

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Basic information

Entry
Database: PDB / ID: 4d7e
TitleAn unprecedented NADPH domain conformation in Lysine Monooxygenase NbtG from Nocardia farcinica
ComponentsL-LYS MONOOXYGENASE
KeywordsOXIDOREDUCTASE / LYSINE HYDROXYLASE / FLAVIN-DEPENDENT MONOOXYGENASES / N-HYDROXYLATING MONOOXYGENASES / SIDEROPHORE / C4A-HYDROPEROXYFLAVIN
Function / homologyL-lysine N6-monooxygenase (NADPH) / L-lysine 6-monooxygenase (NADPH) activity / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / biosynthetic process / FAD/NAD(P)-binding domain superfamily / nucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / L-lysine N6-monooxygenase MbtG
Function and homology information
Biological speciesNOCARDIA FARCINICA IFM 10152 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsBinda, C. / Robinson, R. / Keul, N. / Rodriguez, P. / Robinson, H.H. / Mattevi, A. / Sobrado, P.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: An Unprecedented Nadph Domain Conformation in Lysine Monooxygenase Nbtg Provides Insights Into Uncoupling of Oxygen Consumption from Substrate Hydroxylation.
Authors: Binda, C. / Robinson, R.M. / Martin Del Campo, J.S. / Keul, N.D. / Rodriguez, P.J. / Robinson, H.H. / Mattevi, A. / Sobrado, P.
History
DepositionNov 24, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-LYS MONOOXYGENASE
B: L-LYS MONOOXYGENASE
C: L-LYS MONOOXYGENASE
D: L-LYS MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,5258
Polymers186,3834
Non-polymers3,1424
Water4,288238
1
B: L-LYS MONOOXYGENASE
D: L-LYS MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7634
Polymers93,1912
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-31.4 kcal/mol
Surface area29960 Å2
MethodPISA
2
A: L-LYS MONOOXYGENASE
C: L-LYS MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7634
Polymers93,1912
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-30.1 kcal/mol
Surface area32650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.640, 121.920, 91.860
Angle α, β, γ (deg.)90.00, 97.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
L-LYS MONOOXYGENASE


Mass: 46595.727 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NOCARDIA FARCINICA IFM 10152 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): TOP10 / References: UniProt: Q5Z1T5
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsK184A MUTANT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 7.5
Details: 10% W/V PEG6000, 5% V/V 2, 4-METHYLPENTANDIOL (MPD), 0.1 M HEPES/NAOH PH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.075
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.4→80 Å / Num. obs: 68260 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.3
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
Aimlessdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.4→91.19 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.907 / SU B: 25.517 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R: 0.403 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.28148 2819 4.1 %RANDOM
Rwork0.2076 ---
obs0.21064 65407 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.72 Å2
2---0.54 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.4→91.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11264 0 212 238 11714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911736
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211115
X-RAY DIFFRACTIONr_angle_refined_deg1.71.96815961
X-RAY DIFFRACTIONr_angle_other_deg0.882325440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97251442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08122.998507
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.423151846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7661599
X-RAY DIFFRACTIONr_chiral_restr0.0930.21770
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022709
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8053.8695837
X-RAY DIFFRACTIONr_mcbond_other2.8063.8695836
X-RAY DIFFRACTIONr_mcangle_it4.3875.7857256
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0024.1785899
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 214 -
Rwork0.337 4791 -
obs--98.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0641-0.61910.39121.6427-0.69891.2851-0.0926-0.20950.02730.2670.0843-0.1264-0.2392-0.08480.00840.402-0.00750.16520.21960.00390.108966.214759.77795.898
20.9525-0.31251.08763.86790.20113.75990.2858-0.0541-0.0972-0.1819-0.0723-0.11850.4333-0.3013-0.21350.34020.01610.09790.21660.05950.08773.003735.207783.4367
32.3372-0.2066-1.06970.99360.29081.60030.01960.3897-0.1426-0.0399-0.0108-0.00690.1138-0.3404-0.00880.291-0.0460.17110.3643-0.01010.13460.348732.250543.9452
43.18850.77390.2544.43031.2172.10190.15640.11490.4633-0.04440.0397-0.1433-0.38170.2807-0.1960.2563-0.06030.18510.2568-0.00620.18875.827553.180355.938
50.9957-0.1660.88541.6453-1.03152.4249-0.1982-0.03420.11730.16290.040.0905-0.5077-0.2990.15820.43570.13560.13320.23540.00540.124447.597281.571666.0994
61.7471-0.29520.28015.81030.91572.58380.16030.1781-0.0045-0.17010.0510.14440.1195-0.4233-0.21130.11170.06720.06070.33680.11830.093231.416461.93151.9278
73.08920.8529-1.6950.978-0.34381.71670.178-0.4452-0.12850.2127-0.14620.16060.0434-0.2202-0.03170.3445-0.11240.22510.71570.20030.273131.575424.815472.6319
87.74967.20981.7113.8104-0.0710.79920.56840.0723-0.05730.2825-0.52520.54090.22660.1059-0.04320.29120.12770.24720.5377-0.06070.426922.912447.603675.6347
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 178
2X-RAY DIFFRACTION1A248 - 277
3X-RAY DIFFRACTION1A337 - 500
4X-RAY DIFFRACTION2A179 - 239
5X-RAY DIFFRACTION2A279 - 336
6X-RAY DIFFRACTION3B2 - 178
7X-RAY DIFFRACTION3B249 - 277
8X-RAY DIFFRACTION3B337 - 500
9X-RAY DIFFRACTION4B179 - 238
10X-RAY DIFFRACTION4B280 - 336
11X-RAY DIFFRACTION5C2 - 178
12X-RAY DIFFRACTION5C249 - 272
13X-RAY DIFFRACTION5C337 - 500
14X-RAY DIFFRACTION6C179 - 238
15X-RAY DIFFRACTION6C286 - 336
16X-RAY DIFFRACTION7D2 - 178
17X-RAY DIFFRACTION7D249 - 277
18X-RAY DIFFRACTION7D338 - 500
19X-RAY DIFFRACTION8D179 - 228
20X-RAY DIFFRACTION8D286 - 336

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