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- PDB-6sq8: Structure of amide bond synthetase McbA from Marinactinospora the... -

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Basic information

Entry
Database: PDB / ID: 6sq8
TitleStructure of amide bond synthetase McbA from Marinactinospora thermotolerans
ComponentsFatty acid CoA ligase
KeywordsLIGASE / McbA / amide / ATP / ANL enzyme
Function / homology
Function and homology information


ANL, C-terminal 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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme ...ANL, C-terminal 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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Chem-EQ2 / Fatty acid CoA ligase
Similarity search - Component
Biological speciesMarinactinospora thermotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsRowlinson, B. / Petchey, M. / Grogan, G.
CitationJournal: Acs Catalysis / Year: 2020
Title: Biocatalytic Synthesis of Moclobemide Using the Amide Bond Synthetase McbA Coupled with an ATP Recycling System.
Authors: Petchey, M.R. / Rowlinson, B. / Lloyd, R.C. / Fairlamb, I.J.S. / Grogan, G.
History
DepositionSep 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid CoA ligase
B: Fatty acid CoA ligase
C: Fatty acid CoA ligase
D: Fatty acid CoA ligase
E: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,74915
Polymers265,7415
Non-polymers3,00710
Water8,287460
1
A: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7503
Polymers53,1481
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7503
Polymers53,1481
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7503
Polymers53,1481
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7503
Polymers53,1481
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7503
Polymers53,1481
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.085, 131.028, 196.081
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTHRTHRAA-1 - 4942 - 497
21PROPROTHRTHRBB-1 - 4942 - 497
12PROPROTHRTHRAA-1 - 4942 - 497
22PROPROTHRTHRCC-1 - 4942 - 497
13PROPROPHEPHEAA-1 - 4932 - 496
23PROPROPHEPHEDD-1 - 4932 - 496
14METMETTHRTHRAA1 - 4944 - 497
24METMETTHRTHREE1 - 4944 - 497
15PROPROASPASPBB-1 - 4952 - 498
25PROPROASPASPCC-1 - 4952 - 498
16PROPROTHRTHRBB-1 - 4942 - 497
26PROPROTHRTHRDD-1 - 4942 - 497
17METMETASPASPBB1 - 4954 - 498
27METMETASPASPEE1 - 4954 - 498
18PROPROTHRTHRCC-1 - 4942 - 497
28PROPROTHRTHRDD-1 - 4942 - 497
19METMETASPASPCC1 - 4954 - 498
29METMETASPASPEE1 - 4954 - 498
110METMETTHRTHRDD1 - 4944 - 497
210METMETTHRTHREE1 - 4944 - 497

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Fatty acid CoA ligase


Mass: 53148.266 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinactinospora thermotolerans (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R4R1U5
#2: Chemical
ChemComp-EQ2 / 1-ethanoyl-9~{H}-pyrido[3,4-b]indole-3-carboxylic acid


Mass: 254.241 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H10N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6 M sodium citrate pH 7.5; 6% (w/v) ethylene glycol

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.59→65.54 Å / Num. obs: 95977 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.13 / Net I/σ(I): 6.2
Reflection shellResolution: 2.59→2.66 Å / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6982 / CC1/2: 0.49 / Rpim(I) all: 0.47

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H1B

6h1b


Resolution: 2.59→65.54 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.902 / SU B: 13.662 / SU ML: 0.267 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.597 / ESU R Free: 0.297
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 4768 5 %RANDOM
Rwork0.2128 ---
obs0.2146 91126 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 119.51 Å2 / Biso mean: 38.567 Å2 / Biso min: 2.16 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å20 Å2
2--0.56 Å2-0 Å2
3----2.04 Å2
Refinement stepCycle: final / Resolution: 2.59→65.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17991 0 183 460 18634
Biso mean--58.67 27.65 -
Num. residues----2451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01418641
X-RAY DIFFRACTIONr_bond_other_d0.0010.01716679
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.66125547
X-RAY DIFFRACTIONr_angle_other_deg0.871.62938793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76552441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.40819.748874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.949152611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.25115170
X-RAY DIFFRACTIONr_chiral_restr0.0640.22476
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221500
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023308
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A145910.06
12B145910.06
21A146670.06
22C146670.06
31A146480.07
32D146480.07
41A138630.09
42E138630.09
51B146840.07
52C146840.07
61B145860.07
62D145860.07
71B139980.1
72E139980.1
81C146330.07
82D146330.07
91C139360.1
92E139360.1
101D138480.1
102E138480.1
LS refinement shellResolution: 2.59→2.656 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.339 347 -
Rwork0.344 6536 -
obs--98.54 %

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