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- PDB-6zu3: Crystal structure of a cyclodipeptide synthase from Bacillus ther... -

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Basic information

Entry
Database: PDB / ID: 6zu3
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 / Cyclodipeptide synthase
Function and homology information
Biological speciesBacillus thermoamylovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 21, 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


Theoretical massNumber of molelcules
Total (without water)27,2611
Polymers27,2611
Non-polymers00
Water1,67593
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 area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.840, 79.840, 91.930
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
Details: S33A mutation / Source: (gene. exp.) Bacillus thermoamylovorans (bacteria) / Gene: yvmC, BT1A1_1686 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A090KS30
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.69 Å3/Da / Density % sol: 54.22 %
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 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.78→56.46 Å / Num. obs: 29166 / % possible obs: 100 % / Redundancy: 26.3 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.012 / Rrim(I) all: 0.061 / Net I/σ(I): 27.9 / Num. measured all: 766387
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
1.78-1.8326.42.6865537020980.6240.532.7391.499.9
7.96-56.4620.80.021840640510.0050.02194.299.8

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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: 6ZTU
Resolution: 1.78→56.455 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 1450 4.98 %
Rwork0.183 27656 -
obs0.1849 29106 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.38 Å2 / Biso mean: 45.9466 Å2 / Biso min: 26.87 Å2
Refinement stepCycle: final / Resolution: 1.78→56.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 0 93 2002
Biso mean---49.95 -
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
1.78-1.84360.31961600.26872698
1.8436-1.91740.24961080.21872734
1.9174-2.00470.1941380.18882735
2.0047-2.11040.19881450.17942715
2.1104-2.24260.21921400.17062731
2.2426-2.41580.21851330.18042770
2.4158-2.65890.22751480.17852740
2.6589-3.04360.2281400.18942784
3.0436-3.83450.22321710.18522793
3.8345-56.4550.21161670.17642956
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.1260.0969-0.21840.3992-0.15980.45480.03210.2850.2171-0.1244-0.0099-0.5058-0.22520.37230.00150.4736-0.06880.07830.4497-0.08240.494925.990626.57126.7366
21.2042-0.09330.80741.05431.01232.3259-0.10340.0474-0.1056-0.02670.247-0.2030.32260.19880.00030.36030.004-0.00310.3192-0.01880.361718.547317.244819.2387
30.3022-0.15740.22230.85960.67240.88730.0626-0.718-0.95860.2556-0.068-0.61510.78960.1289-0.00190.6001-0.0105-0.09690.51580.08360.494617.700611.335728.4647
40.44690.3212-0.4880.93950.28961.2046-0.0851-0.3358-0.03910.03530.07580.1086-0.2569-0.1293-0.00020.3024-0.0199-0.00580.3446-0.00440.30417.360627.977922.7053
51.27530.5928-0.53930.3732-0.01870.7697-0.08270.1124-0.3226-0.1927-0.1722-0.05580.42340.0927-0.00560.517-0.0137-0.00280.34880.01310.43221.514311.193810.9303
60.444-0.50760.00670.8576-0.15351.4770.08450.06510.05280.19770.10990.28430.2217-0.12480.00020.362-0.0323-0.03470.32030.00520.35044.001921.358317.7934
71.14240.3083-0.10620.39140.00571.5582-0.06070.20130.032-0.1530.0199-0.1329-0.02230.0890.00120.3917-0.02560.02960.3507-0.03910.344213.265326.68528.6942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 24 )A2 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 77 )A25 - 77
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 102 )A78 - 102
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 135 )A103 - 135
5X-RAY DIFFRACTION5chain 'A' and (resid 136 through 165 )A136 - 165
6X-RAY DIFFRACTION6chain 'A' and (resid 166 through 190 )A166 - 190
7X-RAY DIFFRACTION7chain 'A' and (resid 191 through 231 )A191 - 231

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