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

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Basic information

Entry
Database: PDB / ID: 7qax
TitleCrystal structure of a cyclodipeptide synthase from Parcubacteria bacterium RAAC4_OD1_1, E171Q 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: 2.089 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)27,3341
Polymers27,3341
Non-polymers00
Water27015
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 area11880 Å2
Unit cell
Length a, b, c (Å)102.973, 102.973, 49.812
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: 27333.535 Da / Num. of mol.: 1 / Mutation: E171Q
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.: 15 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
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 PILATUS 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: 2.089→46.051 Å / Num. obs: 222211 / % possible obs: 92.57 % / Redundancy: 14.5 % / CC1/2: 0.999 / Net I/σ(I): 15.8
Reflection shellResolution: 2.09→2.16 Å / Rmerge(I) obs: 1.637 / Num. unique obs: 1565 / CC1/2: 0.331

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Processing

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

7qae
PDB Unreleased entry


Resolution: 2.089→46.051 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2642 737 4.84 %
Rwork0.2187 14478 -
obs0.2209 15215 92.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.12 Å2 / Biso mean: 68.1625 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.089→46.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1862 0 0 15 1877
Biso mean---48.41 -
Num. residues----221
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.089-2.24990.33181470.3027258297
2.2499-2.47630.29361450.2504293599
2.4763-2.83460.26631410.2333285293
2.8346-3.57110.27881460.2573302696
3.5711-46.0510.2511580.1939308394
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)
14.06921.50191.32963.1421-0.54132.58120.03641.0971-0.0623-0.4565-0.09780.0914-0.0830.5992-0.00030.54080.0198-0.08020.63660.00750.408623.182958.15213.8014
20.7599-0.3775-0.59230.38530.18530.5356-0.6707-1.2392-0.01631.20250.20190.05770.0291-0.504-0.00350.5707-0.0451-0.03660.51620.01940.710112.209952.066224.9051
33.30670.59710.60932.34560.36270.90020.34740.7087-0.6151-0.29520.10690.2180.6470.1434-0.00020.540.0119-0.09570.6515-0.10510.589811.753649.9575.9326
45.9187-0.93181.05312.5556-0.40492.33540.1591-0.75380.27550.25670.03230.24850.0451-0.1139-0.00110.5362-0.04650.06110.5706-0.03990.462525.908658.096828.7434
53.99330.15381.67851.24530.56393.2513-0.05550.5019-0.20520.05870.1926-0.2711-0.00630.42360.00110.4548-0.0046-0.02320.5493-0.04540.49231.60856.088413.9037
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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