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- PDB-8jbr: Structure of McyA2-CAPCP -

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Basic information

Entry
Database: PDB / ID: 8jbr
TitleStructure of McyA2-CAPCP
ComponentsMcyA protein
KeywordsTOXIN / NRPSs / microcystin synthase / condensation domain / adenylation doamin
Function / homology
Function and homology information


amide biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity
Similarity search - Function
Microcystin synthetase, domain of unknown function / Microcystin synthetase C terminal / Non-ribosomal peptide synthase / Methyltransferase type 12 / Methyltransferase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain ...Microcystin synthetase, domain of unknown function / Microcystin synthetase C terminal / Non-ribosomal peptide synthase / Methyltransferase type 12 / Methyltransferase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 4'-PHOSPHOPANTETHEINE / McyA protein
Similarity search - Component
Biological speciesMicrocystis aeruginosa PCC 7806 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPeng, Y.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Modular catalytic activity of nonribosomal peptide synthetases depends on the dynamic interaction between adenylation and condensation domains.
Authors: Peng, Y.J. / Chen, Y. / Zhou, C.Z. / Miao, W. / Jiang, Y.L. / Zeng, X. / Zhang, C.C.
History
DepositionMay 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: McyA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2033
Polymers117,3371
Non-polymers8662
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-12 kcal/mol
Surface area45440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.990, 173.990, 78.033
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-2515-

HOH

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Components

#1: Protein McyA protein


Mass: 117337.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microcystis aeruginosa PCC 7806 (bacteria)
Gene: mcyA / Production host: Escherichia coli (E. coli) / References: UniProt: A8YJV7
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C11H23N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 50.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 17% PEG 3350, 0.2 M lithium sulfate , 0.1 M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.5→46.59 Å / Num. obs: 40435 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 9.7 % / Rsym value: 0.118 / Net I/σ(I): 19.058
Reflection shellResolution: 2.5→2.59 Å / Rsym value: 0.108 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.55 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3051 1900 4.7 %RANDOM
Rwork0.265 ---
obs0.2669 40434 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8146 0 52 32 8230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058380
X-RAY DIFFRACTIONf_angle_d0.9111403
X-RAY DIFFRACTIONf_dihedral_angle_d16.6981125
X-RAY DIFFRACTIONf_chiral_restr0.0581295
X-RAY DIFFRACTIONf_plane_restr0.0061467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.32841320.3242691X-RAY DIFFRACTION98
2.56-2.630.39031360.3212730X-RAY DIFFRACTION100
2.63-2.710.34171320.31732724X-RAY DIFFRACTION100
2.71-2.80.38091220.31692780X-RAY DIFFRACTION100
2.8-2.90.32851890.30652687X-RAY DIFFRACTION100
2.9-3.010.3711430.29962730X-RAY DIFFRACTION100
3.01-3.150.33941420.29722762X-RAY DIFFRACTION100
3.15-3.320.3743910.29212776X-RAY DIFFRACTION100
3.32-3.520.31761580.28382724X-RAY DIFFRACTION100
3.52-3.80.2751330.25032752X-RAY DIFFRACTION100
3.8-4.180.29741520.24242745X-RAY DIFFRACTION100
4.18-4.780.29111030.22522808X-RAY DIFFRACTION100
4.78-6.020.23751290.23552781X-RAY DIFFRACTION100
6.02-46.550.23351380.21792844X-RAY DIFFRACTION100

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