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- PDB-7azu: Crystal structure of a cyclodipeptide synthase from Bacillus ther... -

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Basic information

Entry
Database: PDB / ID: 7azu
TitleCrystal structure of a cyclodipeptide synthase from Bacillus thermoamylovorans
ComponentsCyclodipeptide synthase, BtCDPS
KeywordsRNA BINDING PROTEIN / CDPS / cyclodipeptide synthase
Function / homologyCyclodipeptide synthase superfamily / Cyclodipeptide synthase / Cyclodipeptide synthase / aminoacyltransferase activity / (2S)-hexane-1,2-diol / Cyclodipeptide synthase
Function and homology information
Biological speciesBacillus thermoamylovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsHarding, C.J. / Czekster, C.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust210486/Z/18/Z United Kingdom
CitationJournal: Rsc Chem Biol / Year: 2021
Title: Bypassing the requirement for aminoacyl-tRNA by a cyclodipeptide synthase enzyme.
Authors: Harding, C.J. / Sutherland, E. / Hanna, J.G. / Houston, D.R. / Czekster, C.M.
History
DepositionNov 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclodipeptide synthase, BtCDPS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2932
Polymers27,1751
Non-polymers1181
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.780, 79.780, 92.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cyclodipeptide synthase, BtCDPS


Mass: 27175.295 Da / Num. of mol.: 1 / Mutation: R153A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thermoamylovorans (bacteria) / Gene: yvmC, BT1A1_1686 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A090KS30
#2: Chemical ChemComp-0RE / (2S)-hexane-1,2-diol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na Citrate pH 5.5, 37% PEG 550 MME, 5% 1,2-hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→60.5 Å / Num. obs: 28430 / % possible obs: 100 % / Redundancy: 26.4 % / Biso Wilson estimate: 36.46 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.012 / Rrim(I) all: 0.061 / Net I/σ(I): 26.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.8323.92.1391.413600.8330.442.18597.8
4.89-60.5424.20.03178.215900.9990.0060.031100

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZTU

6ztu


Resolution: 1.801→48.208 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2259 1431 5.06 %
Rwork0.2041 26842 -
obs0.2052 28273 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.32 Å2 / Biso mean: 47.4758 Å2 / Biso min: 33.47 Å2
Refinement stepCycle: final / Resolution: 1.801→48.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 8 108 2020
Biso mean--48.4 50.5 -
Num. residues----230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.801-1.8650.37011420.309260699
1.865-1.93970.28391540.2731261499
1.9397-2.0280.3041370.2458263999
2.028-2.13490.24981290.23652643100
2.1349-2.26870.28441380.22612659100
2.2687-2.44380.25381540.22352663100

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