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- PDB-6ztu: Crystal structure of a cyclodipeptide synthase from Bacillus ther... -

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Basic information

Entry
Database: PDB / ID: 6ztu
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: 1.69 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
DepositionJul 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Experimental preparation / Category: citation / citation_author / exptl_crystal_grow
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 / _exptl_crystal_grow.temp
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)27,3802
Polymers27,2611
Non-polymers1181
Water3,423190
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 area11550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.969, 79.969, 92.073
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: 27261.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thermoamylovorans (bacteria) / Gene: yvmC, BT1A1_1686 / Production host: Escherichia coli (E. coli) / 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 / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na Citrate pH 5.5, 37.5 % 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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.69→60.37 Å / Num. obs: 34140 / % possible obs: 100 % / Redundancy: 25.1 % / CC1/2: 1 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.019 / Rrim(I) all: 0.098 / Net I/σ(I): 19.4 / Num. measured all: 857699 / Scaling rejects: 757
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.69-1.7316.72.8114142424850.4880.6992.8991.1
7.56-60.3722.50.0271061347110.0060.02885.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
Aimlessdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3oqi

3oqi


Resolution: 1.69→56.547 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2119 1659 4.87 %
Rwork0.1896 32395 -
obs0.1907 34054 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.84 Å2 / Biso mean: 33.9025 Å2 / Biso min: 18.49 Å2
Refinement stepCycle: final / Resolution: 1.69→56.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 8 190 2108
Biso mean--38.33 41.92 -
Num. residues----230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.6901-1.73980.32671550.30062642
1.7398-1.7960.28961180.25942656
1.796-1.86020.26921320.23312662
1.8602-1.93460.26891250.21392663
1.9346-2.02270.23481270.21052658
2.0227-2.12930.26481380.20212663
2.1293-2.26280.22211420.19342689
2.2628-2.43750.25291220.20332698
2.4375-2.68280.22751440.19552695
2.6828-3.07090.23341530.1962705
3.0709-3.86890.18791480.17492755
3.8689-56.5470.1731550.16982909

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