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- PDB-7qau: Crystal structure of a cyclodipeptide synthase from Parcubacteria... -

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Basic information

Entry
Database: PDB / ID: 7qau
TitleCrystal structure of a cyclodipeptide synthase from Parcubacteria bacterium RAAC4_OD1_1, D58N mutant
ComponentsCyclodipeptide synthase
KeywordsLIGASE / Cyclodipeptide synthase
Function / homologyCyclodipeptide synthase superfamily / Cyclodipeptide synthase / Cyclodipeptide synthase / aminoacyltransferase activity / Cyclodipeptide synthase
Function and homology information
Biological speciesParcubacteria bacterium RAAC4_OD1_1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSutherland, E. / Harding, C.J. / Czekster, C.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privatePhD-CT-18-41 United Kingdom
CitationJournal: Commun Chem / Year: 2022
Title: Active site remodelling of a cyclodipeptide synthase redefines substrate scope.
Authors: Sutherland, E. / Harding, C.J. / Czekster, C.M.
History
DepositionNov 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclodipeptide synthase


Theoretical massNumber of molelcules
Total (without water)28,1621
Polymers28,1621
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11810 Å2
Unit cell
Length a, b, c (Å)103.440, 103.440, 49.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Cyclodipeptide synthase


Mass: 28162.416 Da / Num. of mol.: 1 / Mutation: D58N
Source method: isolated from a genetically manipulated source
Details: C-terminal His Tag (EHHHHHH)
Source: (gene. exp.) Parcubacteria bacterium RAAC4_OD1_1 (bacteria)
Gene: O210_OD1C00001G0241 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V7PYQ5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.27 M Ammonium Sulfate 0.1 M Sodium Acetate pH 5.17

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.3→46.26 Å / Num. obs: 12429 / % possible obs: 99.3 % / Redundancy: 25.1 % / CC1/2: 1 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.018 / Rrim(I) all: 0.089 / Net I/σ(I): 27 / Num. measured all: 311398 / Scaling rejects: 196
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.3624.81.171218978840.90.2371.195499
10.29-46.26190.039336617710.0090.0455.299.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QAE

7qae
PDB Unreleased entry


Resolution: 2.3→46.26 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 600 4.84 %
Rwork0.2096 11799 -
obs0.2115 12399 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.91 Å2 / Biso mean: 69.7855 Å2 / Biso min: 39.22 Å2
Refinement stepCycle: final / Resolution: 2.3→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1814 0 0 11 1825
Biso mean---58.02 -
Num. residues----215
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3001-2.53150.27271530.2211284698
2.5315-2.89780.26621520.2195288499
2.8978-3.65070.29631420.2388294999
3.6507-46.260.2221530.195312099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.11140.29160.6916.0011-0.06972.94610.08660.90240.0317-0.46180.1051-0.0294-0.17470.7619-0.13150.5112-0.0122-0.04530.5854-0.09190.346721.536657.97763.3919
27.1343-0.430.38993.22810.18167.2041-0.0633-1.097-0.29010.4752-0.10930.3146-0.1383-0.23420.22280.5495-0.04880.02990.610.06190.644712.209852.245724.8893
35.85140.29312.91151.5792-0.67592.87860.46430.2505-0.6499-0.17490.06140.14330.62710.0585-0.49060.44230.0381-0.01730.3702-0.05010.518.340449.615513.9692
46.5849-2.6292-2.32423.88931.72461.1490.1765-0.72270.8760.1531-0.12430.4416-0.0827-0.5264-0.12010.6062-0.00690.05460.6736-0.17580.672224.094862.486728.8051
55.1657-0.62451.97671.4405-0.49554.493-0.12340.6079-0.27960.05030.2298-0.1987-0.17130.4284-0.09310.4637-0.012-0.0170.495-0.06610.463631.603956.57113.841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 58 )A1 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 83 )A59 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 134 )A84 - 134
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 176 )A135 - 176
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 230 )A177 - 230

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