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- PDB-7poa: An Irreversible, Promiscuous and Highly Thermostable Claisen-Cond... -

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Basic information

Entry
Database: PDB / ID: 7poa
TitleAn Irreversible, Promiscuous and Highly Thermostable Claisen-Condensation Biocatalyst Drives the Synthesis of Substituted Pyrroles
Components8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase
KeywordsSYNTHASE / Biocatalyst / cascade / chemo-enzymatic / thermophilic / promiscuous / alpha-oxoamine synthase / pyrrole
Function / homology
Function and homology information


glycine C-acetyltransferase / glycine C-acetyltransferase activity / 8-amino-7-oxononanoate synthase / 8-amino-7-oxononanoate synthase activity / biotin biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Putative 8-amino-7-oxononanoate synthase, Archaea/Firmicutes type / 8-amino-7-oxononanoate synthase, Archaea/Proteobacteria type / : / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Putative 8-amino-7-oxononanoate synthase, Archaea/Firmicutes type / 8-amino-7-oxononanoate synthase, Archaea/Proteobacteria type / : / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBasle, A. / Ashley, B. / Campopiano, D. / Marles-Wright, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J01446X/1 United Kingdom
CitationJournal: Acs Sustain Chem Eng / Year: 2023
Title: Versatile Chemo-Biocatalytic Cascade Driven by a Thermophilic and Irreversible C-C Bond-Forming alpha-Oxoamine Synthase.
Authors: Ashley, B. / Basle, A. / Sajjad, M. / El Ashram, A. / Kelis, P. / Marles-Wright, J. / Campopiano, D.J.
History
DepositionSep 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase
B: 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9977
Polymers93,1702
Non-polymers8275
Water8,755486
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint-93 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.410, 63.890, 65.910
Angle α, β, γ (deg.)64.740, 70.500, 68.120
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 3 - 395 / Label seq-ID: 28 - 420

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase / AONS/AKB ligase / 7-keto-8-amino-pelargonic acid synthase / 7-KAP synthase / KAPA synthase / 8- ...AONS/AKB ligase / 7-keto-8-amino-pelargonic acid synthase / 7-KAP synthase / KAPA synthase / 8-amino-7-ketopelargonate synthase / Alpha-oxoamine synthase / Glycine acetyltransferase


Mass: 46585.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TTHA1582 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SHZ8, glycine C-acetyltransferase, 8-amino-7-oxononanoate synthase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 30 mM sodium nitrate, 30 mM sodium phosphate, 30 mM ammonium sulfate, 100 mM Hepes/MOPS pH 7.5, 12.5 % (v/v) MPD, 12.5 % (w/v) PEG 1000 and 12.5 % (w/v) PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.6→55.634 Å / Num. obs: 97563 / % possible obs: 96.2 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.034 / Rrim(I) all: 0.062 / Net I/σ(I): 15.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.76-55.637.20.018975630.9960.0110.021
1.6-1.636.21.16142860.6040.7771.406

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHASERphasing
Aimlessdata scaling
pointlessdata scaling
Cootmodel building
BUCCANEERmodel building
MolProbitymodel building
xia2data scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TQX

3tqx


Resolution: 1.6→55.634 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.165 / SU B: 8.454 / SU ML: 0.124 / Average fsc free: 0.8488 / Average fsc work: 0.8975 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2395 4803 4.923 %
Rwork0.1686 92756 -
all0.172 --
obs-97559 96.16 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.368 Å2
Baniso -1Baniso -2Baniso -3
1-0.005 Å2-1.814 Å2-0.537 Å2
2--1.999 Å21.814 Å2
3----2.106 Å2
Refinement stepCycle: LAST / Resolution: 1.6→55.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6135 0 51 488 6674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136312
X-RAY DIFFRACTIONr_bond_other_d0.0050.0176183
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.6428540
X-RAY DIFFRACTIONr_angle_other_deg1.4571.57914201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7645792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.69921.015325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.629151085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8281552
X-RAY DIFFRACTIONr_chiral_restr0.0920.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027067
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021419
X-RAY DIFFRACTIONr_nbd_refined0.2110.21347
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.25760
X-RAY DIFFRACTIONr_nbtor_refined0.1670.23040
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22928
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2420
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.3560.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3320.28
X-RAY DIFFRACTIONr_nbd_other0.1880.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1660.213
X-RAY DIFFRACTIONr_mcbond_it4.5582.6563168
X-RAY DIFFRACTIONr_mcbond_other4.5562.6553167
X-RAY DIFFRACTIONr_mcangle_it5.3494.0063957
X-RAY DIFFRACTIONr_mcangle_other5.3494.0073958
X-RAY DIFFRACTIONr_scbond_it6.6483.133144
X-RAY DIFFRACTIONr_scbond_other6.6243.1263141
X-RAY DIFFRACTIONr_scangle_it7.594.5244582
X-RAY DIFFRACTIONr_scangle_other7.5464.5194577
X-RAY DIFFRACTIONr_lrange_it7.09732.9157135
X-RAY DIFFRACTIONr_lrange_other7.09632.9157136
X-RAY DIFFRACTIONr_rigid_bond_restr6.166312495
X-RAY DIFFRACTIONr_ncsr_local_group_10.0670.0512445
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.06750.05007
12BX-RAY DIFFRACTIONLocal ncs0.06750.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.6-1.6420.363410.27562130.27975040.6980.78787.34010.258
1.642-1.6860.3383480.23565030.2473480.7680.84693.23630.213
1.686-1.7350.3383140.20764720.21371010.8170.88395.5640.181
1.735-1.7890.2863720.20662530.2169070.8150.87495.91720.177
1.789-1.8470.3352960.1960880.19766450.8290.89496.07220.161
1.847-1.9120.2892920.17559520.1864680.8460.90496.53680.146
1.912-1.9840.2713270.1757750.17663160.870.91396.61180.146
1.984-2.0650.2722650.18555380.18959960.8370.88496.78120.162
2.065-2.1570.2792660.16452700.16957080.8660.92296.98670.146
2.157-2.2620.2672740.15350860.15955270.890.92896.97850.135
2.262-2.3840.2492460.16948920.17352670.8770.997.55080.153
2.384-2.5280.2492550.15345880.15849590.8750.92597.66080.141
2.528-2.7020.2491880.17443650.17746520.8660.90297.87190.165
2.702-2.9180.2171720.1740530.17243140.9080.9297.9370.166
2.918-3.1960.2432030.18937600.19240250.8710.998.45960.191
3.196-3.5720.2291940.17333640.17636030.9180.94498.7510.176
3.572-4.1220.191450.15629990.15831780.9330.94898.93010.169
4.122-5.0410.171300.12125400.12326900.9670.97799.25650.139
5.041-7.10.2361050.16819660.17120930.9380.95898.94890.193
7.1-55.6340.179700.16610790.16611530.9580.96299.65310.188

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