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- PDB-7us3: Structure of Putrescine N-hydroxylase Involved Complexed with NADP+ -

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Basic information

Entry
Database: PDB / ID: 7us3
TitleStructure of Putrescine N-hydroxylase Involved Complexed with NADP+
ComponentsPutrescine N-hydroxylase
KeywordsFLAVOPROTEIN / Monooxygenase / Putrescine N-hydroxylase
Function / homologyL-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / cellular biosynthetic process / organonitrogen compound biosynthetic process / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TRIETHYLENE GLYCOL / Alcaligin biosynthesis protein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTanner, J.J. / Bogner, A.N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2003986 United States
National Science Foundation (NSF, United States)CHE-2003658 United States
CitationJournal: Biochemistry / Year: 2022
Title: Kinetic and Structural Characterization of a Flavin-Dependent Putrescine N -Hydroxylase from Acinetobacter baumannii.
Authors: Lyons, N.S. / Bogner, A.N. / Tanner, J.J. / Sobrado, P.
History
DepositionApr 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putrescine N-hydroxylase
B: Putrescine N-hydroxylase
C: Putrescine N-hydroxylase
D: Putrescine N-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,84415
Polymers214,2344
Non-polymers6,61011
Water10,863603
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32710 Å2
ΔGint-141 kcal/mol
Surface area59780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.827, 126.314, 140.248
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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
Putrescine N-hydroxylase / Putrescine N-hydroxylase


Mass: 53558.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: AUO97_01770 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E3MAZ6

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Non-polymers , 5 types, 614 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 / Feature type: SUBJECT OF INVESTIGATION / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 603 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M ammonium sulfate, 0.05 M Bis-Tris pH 6.5, and 30% pentaerythritol ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→140.25 Å / Num. obs: 111523 / % possible obs: 99.3 % / Redundancy: 8.1 % / Biso Wilson estimate: 39.11 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.095 / Rrim(I) all: 0.268 / Net I/σ(I): 8.8 / Num. measured all: 902459 / Scaling rejects: 197
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.246.61.3833219649080.4660.571.5021.389
12.07-140.256.40.07950177870.9870.0330.08626.898.1

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6xbb

6xbb


Resolution: 2.2→88.79 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2225 5590 5.02 %
Rwork0.1817 105682 -
obs0.1837 111272 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.03 Å2 / Biso mean: 38.5458 Å2 / Biso min: 24.9 Å2
Refinement stepCycle: final / Resolution: 2.2→88.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13754 0 437 603 14794
Biso mean--40.48 36.91 -
Num. residues----1712
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.230.32681840.30642908309283
2.23-2.260.33882000.27953430363099
2.26-2.280.3221710.26553467363898
2.28-2.310.30991720.253435673739100
2.31-2.340.27691660.238535133679100
2.34-2.370.26181740.22735263700100
2.37-2.410.28511940.22334943688100
2.41-2.440.27961600.219835233683100
2.44-2.480.28041710.212135553726100
2.48-2.520.28381690.212435143683100
2.52-2.570.30361670.209735713738100
2.57-2.610.26972000.201735013701100
2.61-2.660.26392090.20334913700100
2.66-2.720.24831760.206935353711100
2.72-2.780.26021680.208335513719100
2.78-2.840.26842250.216134883713100
2.84-2.910.24771860.215735573743100
2.91-2.990.24122050.201935063711100
2.99-3.080.25131640.208435603724100
3.08-3.180.2651950.205235293724100
3.18-3.290.26271610.20873534369599
3.29-3.420.24161970.202735473744100
3.42-3.580.23631950.186635463741100
3.58-3.770.20352090.168935583767100
3.77-4.010.18271890.156935573746100
4.01-4.310.16872130.139635543767100
4.31-4.750.15841990.132635743773100
4.75-5.440.18692010.138636073808100
5.44-6.850.21021940.166636463840100
6.85-88.790.14911760.13743773394998
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)
10.38180.17230.01290.5759-0.12490.49090.00820.04-0.04480.05160.00660.12740.008-0.0713-0.0180.25890.00770.01290.2659-0.00250.3016-27.86384.8384-11.2897
20.45330.26630.03670.5999-0.04670.2625-0.01130.0961-0.0079-0.06870.0033-0.079-0.02370.12090.0070.2865-0.00440.00710.33820.01930.276516.382721.4313-28.1552
30.29430.14-0.06770.5775-0.09180.27370.0149-0.09350.08770.1113-0.0007-0.0176-0.09920.0794-0.01390.3191-0.01590.00460.3051-0.01450.3041-4.12129.670110.191
40.46360.1510.08470.58680.00850.29770.00410.006-0.20040.0199-0.0029-0.1820.08250.1117-0.00780.28990.0314-0.01460.28050.01150.377612.1679-13.8604-9.0169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A')A0
2X-RAY DIFFRACTION2(chain 'B')B0
3X-RAY DIFFRACTION3(chain 'C')C0
4X-RAY DIFFRACTION4(chain 'D')D0

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