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

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Basic information

Entry
Database: PDB / ID: 7qaq
TitleCrystal structure of a cyclodipeptide synthase from Parcubacteria bacterium RAAC4_OD1_1, E174A mutant
ComponentsCyclodipeptide synthase
KeywordsLIGASE / Cyclodipeptide synthase
Function / homologyCyclodipeptide synthase / Cyclodipeptide synthase / Cyclodipeptide synthase / Cyclodipeptide synthase superfamily / aminoacyltransferase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Cyclodipeptide synthase
Function and homology information
Biological speciesParcubacteria bacterium RAAC4_OD1_1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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)27,2761
Polymers27,2761
Non-polymers00
Water43224
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 area11770 Å2
Unit cell
Length a, b, c (Å)102.600, 102.600, 49.860
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: 27276.484 Da / Num. of mol.: 1 / Mutation: E174A
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


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
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: 2.4→51.3 Å / Num. obs: 10919 / % possible obs: 100 % / Redundancy: 23.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.032 / Rrim(I) all: 0.156 / Net I/σ(I): 26.1 / Num. measured all: 260322 / Scaling rejects: 4694
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
2.4-2.4623.60.711185147840.9590.1470.7276.999.9
10.73-51.316.40.048268816410.0120.0546.399.6

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Processing

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

7qae
PDB Unreleased entry


Resolution: 2.4→45.884 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 544 5 %
Rwork0.1929 10342 -
obs0.1953 10886 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.49 Å2 / Biso mean: 55.3753 Å2 / Biso min: 23.48 Å2
Refinement stepCycle: final / Resolution: 2.4→45.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 0 24 1834
Biso mean---50.47 -
Num. residues----215
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4-2.64160.30631310.21832535
2.6416-3.02370.30491350.22282527
3.0237-3.80930.26211410.19752566
3.8093-45.8840.19871370.17742714
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)
15.6126-1.4389-0.35837.01471.27154.30530.07510.7442-0.0368-0.5680.0121-0.0986-0.17130.7240.02010.3407-0.0325-0.060.4788-0.04690.24221.789357.06223.5028
27.5350.98141.37912.13151.68231.8551-0.2796-0.7851-0.07740.5290.30590.4053-0.74980.0495-0.05240.438-0.06730.01840.42020.09360.484812.248251.539324.9367
36.0032-0.45372.66762.6061-0.50455.60070.21380.3292-0.2796-0.32660.07750.30150.4257-0.0259-0.08110.3278-0.0281-0.08160.2984-0.05490.42711.868649.51226.0406
46.39-1.1656-1.02474.06880.73883.31540.1947-0.81090.4450.35890.2180.1737-0.0368-0.1929-0.26360.3644-0.03110.05770.4388-0.01080.443726.052957.590728.8021
54.9987-0.04522.2991.82850.53825.54190.05160.5419-0.2528-0.03830.1178-0.23880.14470.3412-0.17780.2786-0.01720.00020.3249-0.04750.297231.865355.530313.9106
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 117 )A84 - 117
4X-RAY DIFFRACTION4chain 'A' and (resid 118 through 176 )A118 - 176
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 230 )A177 - 230

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