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- PDB-8g96: Adenylation domain structure from NRPS-like Delta-Poly-L-Ornithin... -

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Basic information

Entry
Database: PDB / ID: 8g96
TitleAdenylation domain structure from NRPS-like Delta-Poly-L-Ornithine synthetase (L-Ornithine bound)
ComponentsDimodular nonribosomal peptide synthase
KeywordsLIGASE / Adenylation domain / NRPS / delta-poly-L-ornithine synthetase / nonribosomal peptide synthetase
Function / homology
Function and homology information


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, C-terminal domain superfamily ...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, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
L-ornithine / Dimodular nonribosomal peptide synthase
Similarity search - Component
Biological speciesAcinetobacter baumannii AB307-0294 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)92,5676
Polymers92,1192
Non-polymers4494
Water2,234124
1
A: Dimodular nonribosomal peptide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1922
Polymers46,0591
Non-polymers1321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dimodular nonribosomal peptide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3764
Polymers46,0591
Non-polymers3163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.975, 92.785, 152.644
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 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 6 - 410 / Label seq-ID: 8 - 412

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and (resid 6 through 283 or (resid 284...AA
22chain 'B'BB

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Components

#1: Protein Dimodular nonribosomal peptide synthase


Mass: 46059.473 Da / Num. of mol.: 2 / Fragment: residues 1-412
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-ORN / L-ornithine / Ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.3→79.29 Å / Num. obs: 39481 / % possible obs: 95.41 % / Redundancy: 12.8 % / Biso Wilson estimate: 55.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1403 / Rpim(I) all: 0.04061 / Net I/σ(I): 13.35
Reflection shellResolution: 2.3→2.37 Å / Num. unique obs: 4052 / CC1/2: 0.416 / Rpim(I) all: 0.9639

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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: 2.3→79.29 Å / SU ML: 0.431 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.8212 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2377 1998 5.06 %
Rwork0.2061 37453 -
obs0.2077 39451 95.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.12 Å2
Refinement stepCycle: LAST / Resolution: 2.3→79.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6336 0 30 124 6490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00366510
X-RAY DIFFRACTIONf_angle_d0.78898864
X-RAY DIFFRACTIONf_chiral_restr0.04821016
X-RAY DIFFRACTIONf_plane_restr0.00511136
X-RAY DIFFRACTIONf_dihedral_angle_d11.69193904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.43211460.4142739X-RAY DIFFRACTION99.93
2.35-2.420.43061470.37552758X-RAY DIFFRACTION100
2.42-2.490.39591480.35722762X-RAY DIFFRACTION99.97
2.49-2.570.3281480.31362774X-RAY DIFFRACTION99.93
2.57-2.660.33761210.29872286X-RAY DIFFRACTION98.29
2.66-2.770.3343980.30381798X-RAY DIFFRACTION94.05
2.77-2.890.32041480.27282781X-RAY DIFFRACTION99.8
2.89-3.050.28181490.25942796X-RAY DIFFRACTION99.93
3.05-3.240.33971480.23722779X-RAY DIFFRACTION99.8
3.24-3.490.27321490.21732785X-RAY DIFFRACTION100
3.49-3.840.22051310.19452485X-RAY DIFFRACTION88.14
3.84-4.390.19281520.16282843X-RAY DIFFRACTION100
4.39-5.530.17041520.15022856X-RAY DIFFRACTION100
5.53-79.290.18331610.1653011X-RAY DIFFRACTION99.91
Refinement TLS params.Method: refined / Origin x: 16.3574681316 Å / Origin y: 2.23973585696 Å / Origin z: -10.8944945521 Å
111213212223313233
T0.375184726398 Å2-0.012847470355 Å2-0.0196392732431 Å2-0.429832632402 Å20.00464315022452 Å2--0.515340561695 Å2
L0.731053666213 °2-0.604361358397 °21.15189675797 °2-0.768942521142 °2-0.895118446907 °2--4.07228993112 °2
S-0.0888916154007 Å °0.0648634885018 Å °0.118471911556 Å °0.0167597422977 Å °-0.109475502604 Å °-0.0998375102115 Å °-0.0453094322473 Å °0.100931101226 Å °0.166212868132 Å °
Refinement TLS groupSelection details: all

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