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- PDB-8g98: Adenylation domain structure from NRPS-like Delta-Poly-L-Ornithin... -

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Basic information

Entry
Database: PDB / ID: 8g98
TitleAdenylation domain structure from NRPS-like Delta-Poly-L-Ornithine synthetase (L-Lysine bound)
ComponentsDimodular nonribosomal peptide synthase
KeywordsLIGASE / Adenylation domain / NRPS / delta-poly-L-ornithine synthetase / nonribosomal peptide synthetase
Function / homology
Function and homology information


Ligases; Forming carbon-nitrogen bonds / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / ligase activity / phosphopantetheine binding / plasma membrane / cytoplasm
Similarity search - Function
Non-ribosomal peptide synthetase, C-terminal / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Trimeric LpxA-like superfamily / AMP-dependent synthetase/ligase / AMP-binding enzyme ...Non-ribosomal peptide synthetase, C-terminal / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Trimeric LpxA-like superfamily / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
LYSINE / Delta-poly-L-ornithine synthetase
Similarity search - Component
Biological speciesAcinetobacter baumannii AB307-0294 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsPatel, K.D. / Gulick, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136235 United States
CitationJournal: Commun Biol / Year: 2023
Title: Structural and functional insights into delta-poly-L-ornithine polymer biosynthesis from Acinetobacter baumannii.
Authors: Patel, K.D. / Gulick, A.M.
History
DepositionFeb 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dimodular nonribosomal peptide synthase
B: Dimodular nonribosomal peptide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,14115
Polymers91,8892
Non-polymers1,25213
Water1,35175
1
A: Dimodular nonribosomal peptide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4606
Polymers45,9441
Non-polymers5165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dimodular nonribosomal peptide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6819
Polymers45,9441
Non-polymers7378
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.480, 91.978, 152.246
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHR(chain 'A' and ((resid 8 through 9 and (name N...AA8 - 17210 - 174
12LYSLYSARGARG(chain 'A' and ((resid 8 through 9 and (name N...AA178 - 410180 - 412
23THRTHRTHRTHR(chain 'B' and (resid 8 through 129 or (resid 130...BB8 - 17210 - 174
24LYSLYSARGARG(chain 'B' and (resid 8 through 129 or (resid 130...BB178 - 410180 - 412

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Components

#1: Protein Dimodular nonribosomal peptide synthase


Mass: 45944.387 Da / Num. of mol.: 2 / Fragment: residues 1-413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii AB307-0294 (bacteria)
Gene: dhbF_1, ABBFA_00818 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5K6CNB8
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50.8 % / Description: Long rods
Crystal growTemperature: 293.15 K / Method: microbatch / pH: 7 / Details: 0.1 M Amm Bromide, 0.1 M BTP pH 7.0, 24% PEG 20K

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2.49→58.64 Å / Num. obs: 31880 / % possible obs: 99.53 % / Redundancy: 12.8 % / Biso Wilson estimate: 62.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1269 / Rpim(I) all: 0.0368 / Net I/σ(I): 15.54
Reflection shellResolution: 2.49→2.57 Å / Num. unique obs: 3069 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Coot0.9.5model building
AutoProcessdata reduction
PHASERphasing
autoPROCdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8G95

8g95


Resolution: 2.49→58.64 Å / SU ML: 0.3638 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0538 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2487 1999 6.27 %
Rwork0.195 29870 -
obs0.1984 31869 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.37 Å2
Refinement stepCycle: LAST / Resolution: 2.49→58.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6104 0 82 75 6261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00796319
X-RAY DIFFRACTIONf_angle_d0.96558619
X-RAY DIFFRACTIONf_chiral_restr0.05551002
X-RAY DIFFRACTIONf_plane_restr0.00681097
X-RAY DIFFRACTIONf_dihedral_angle_d11.27283747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.550.34671380.3212065X-RAY DIFFRACTION97.82
2.55-2.620.34081390.2942074X-RAY DIFFRACTION99.1
2.62-2.70.30361410.2852100X-RAY DIFFRACTION99.42
2.7-2.780.32481400.28742101X-RAY DIFFRACTION99.56
2.78-2.880.36041400.26732099X-RAY DIFFRACTION99.38
2.88-30.3251410.25532111X-RAY DIFFRACTION99.6
3-3.140.28211420.24452110X-RAY DIFFRACTION99.73
3.14-3.30.28711430.21422135X-RAY DIFFRACTION99.74
3.3-3.510.24461420.21182125X-RAY DIFFRACTION99.82
3.51-3.780.25011430.17872138X-RAY DIFFRACTION99.91
3.78-4.160.20461440.15942142X-RAY DIFFRACTION99.78
4.16-4.760.20111440.15852161X-RAY DIFFRACTION99.78
4.76-60.23531470.17382194X-RAY DIFFRACTION100
6-58.640.23421550.17572315X-RAY DIFFRACTION99.76
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)
12.58830749698-0.6429314572951.428729909721.22816776133-1.234130125594.57037220951-0.3132847040720.3367003922030.198824751760.217950894585-0.067057642522-0.379005843678-0.4210547760131.003108581710.4046308804350.507884462706-0.119452638776-0.09442030686740.6308977534050.04021506770840.57660543810533.13326967221.410766581026.42386807196
23.01969701088-1.215283076281.916888539743.11765079214-1.452054343956.14596418077-0.0670881202536-0.0070726398339-0.167970092065-0.0830229968502-0.0410331694006-0.190686636160.1865867949090.06370566655950.04394968079470.404049120314-0.049352141044-0.009811941256830.569441587292-0.01321189385040.58242419695121.6693898829-4.62043927242.90351708337
31.63484426246-0.8038659552330.952600771721.77930956571-0.3664519080963.93438584939-0.556969562949-0.3797757315720.4111357821990.6851581288370.283025248840.0888195572769-1.70244052179-0.6330047150730.3600601917290.9702185441260.266137975128-0.1531139991760.562075019944-0.05171749500570.6407572670316.168545013312.974187806513.8324291297
42.735803322420.4690447021221.866408369171.53751302875-1.080475218394.89653697021-0.0977862694822-0.405298284362-0.4142861622470.1335075878880.3878713211610.3667995189740.304694653234-1.14050481431-0.2472437240450.435706469448-0.06264996682730.02726642190870.764702055320.08978511256690.5744554002696.2215283715-7.963173679255.74563098356
52.47386213759-0.892996410241.798124664691.70274177796-0.9653958043945.13500601008-0.3293887730150.07089091700980.54777429726-0.0392088759023-0.277233973232-0.0738455667753-1.14925149547-0.07933100116260.4241972742320.7010127472390.0574528258408-0.120469615420.4603147528580.07377436584640.59052041822910.565314130116.580886494-29.962529395
62.08675836894-0.6138531435591.444762451822.10715969744-0.7298748989845.882065707440.3632288947690.00395097931571-0.0378824631369-0.340573231406-0.3245904165-0.04475881337950.8972190595880.281011644506-0.03464483968580.5612652784340.124515256041-0.05864280848140.516112504399-0.0001763022125080.47913539117812.7268766671-3.88625255349-29.086691633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 159 )
2X-RAY DIFFRACTION2chain 'A' and (resid 160 through 200 )
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 294 )
4X-RAY DIFFRACTION4chain 'A' and (resid 295 through 411 )
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 159 )
6X-RAY DIFFRACTION6chain 'B' and (resid 160 through 411 )

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