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- PDB-5ymr: The Crystal Structure of IseG -

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Basic information

Entry
Database: PDB / ID: 5ymr
TitleThe Crystal Structure of IseG
ComponentsFormate acetyltransferase
KeywordsLYASE / Isethionate / glycyl radical enzyme / C-S bond cleavage
Function / homology
Function and homology information


Lyases; Carbon-sulfur lyases / alkanesulfonate catabolic process / transferase activity / lyase activity
Similarity search - Function
Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain / Glycine radical domain profile. / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 ...Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain / Glycine radical domain profile. / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-hydroxyethylsulfonic acid / Isethionate sulfite-lyase
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLin, L. / Zhang, J. / Xing, M. / Hua, G. / Guo, C. / Hu, Y. / Wei, Y. / Ang, E. / Zhao, H. / Zhang, Y. / Yuchi, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation of China31570060 China
National Key Research and Development Program of China2017YFD0201403 China
CitationJournal: Nat Commun / Year: 2019
Title: Radical-mediated C-S bond cleavage in C2 sulfonate degradation by anaerobic bacteria.
Authors: Xing, M. / Wei, Y. / Zhou, Y. / Zhang, J. / Lin, L. / Hu, Y. / Hua, G. / N Nanjaraj Urs, A. / Liu, D. / Wang, F. / Guo, C. / Tong, Y. / Li, M. / Liu, Y. / Ang, E.L. / Zhao, H. / Yuchi, Z. / Zhang, Y.
History
DepositionOct 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Formate acetyltransferase
D: Formate acetyltransferase
C: Formate acetyltransferase
A: Formate acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,91514
Polymers365,8584
Non-polymers1,05710
Water13,277737
1
B: Formate acetyltransferase
A: Formate acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,5508
Polymers182,9292
Non-polymers6216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-11 kcal/mol
Surface area49610 Å2
MethodPISA
2
D: Formate acetyltransferase
C: Formate acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,3656
Polymers182,9292
Non-polymers4364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-13 kcal/mol
Surface area50270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.111, 159.444, 115.378
Angle α, β, γ (deg.)90.00, 91.66, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND ((RESID 32 THROUGH 33 AND (NAME N...
211(CHAIN B AND ((RESID 32 THROUGH 33 AND (NAME N...
311(CHAIN C AND ((RESID 32 THROUGH 33 AND (NAME N...
411(CHAIN D AND (RESID 32 THROUGH 35 OR (RESID 36...

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Components

#1: Protein
Formate acetyltransferase


Mass: 91464.477 Da / Num. of mol.: 4 / Mutation: E133A/D134A/R136A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (bacteria)
Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Gene: DVU_2824 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q727N1
#2: Chemical
ChemComp-8X3 / 2-hydroxyethylsulfonic acid / 2-oxidanylethanesulfonic acid / Isethionic acid


Mass: 126.132 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O4S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 737 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M sodium malonate dibasic monohydrate, 0.1M Bis-Tris propane, pH 8.5, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.398→50 Å / Num. obs: 153197 / % possible obs: 98.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 24.64 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 5.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.559 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.27 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.47
RfactorNum. reflection% reflection
Rfree0.262 15290 9.99 %
Rwork0.212 --
obs0.217 153010 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.22 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24931 0 64 737 25732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00825617
X-RAY DIFFRACTIONf_angle_d0.89734816
X-RAY DIFFRACTIONf_dihedral_angle_d15.15115172
X-RAY DIFFRACTIONf_chiral_restr0.0533775
X-RAY DIFFRACTIONf_plane_restr0.0074540
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A14869X-RAY DIFFRACTIONPOSITIONAL
12B14869X-RAY DIFFRACTIONPOSITIONAL
13C14869X-RAY DIFFRACTIONPOSITIONAL
14D14869X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3979-2.42510.33694510.26153797X-RAY DIFFRACTION83
2.4251-2.45370.31715200.24014620X-RAY DIFFRACTION98
2.4537-2.48360.3214900.24084572X-RAY DIFFRACTION99
2.4836-2.5150.32645090.23914594X-RAY DIFFRACTION99
2.515-2.54810.30624930.23824590X-RAY DIFFRACTION99
2.5481-2.5830.3075180.2254584X-RAY DIFFRACTION99
2.583-2.61990.30294960.22984669X-RAY DIFFRACTION99
2.6199-2.6590.31185330.24844538X-RAY DIFFRACTION99
2.659-2.70060.30864920.23374614X-RAY DIFFRACTION99
2.7006-2.74480.30095210.22414575X-RAY DIFFRACTION99
2.7448-2.79220.30465200.23594565X-RAY DIFFRACTION99
2.7922-2.84290.31224950.23154627X-RAY DIFFRACTION99
2.8429-2.89760.31635100.2434627X-RAY DIFFRACTION99
2.8976-2.95670.34075380.23954581X-RAY DIFFRACTION99
2.9567-3.0210.29134870.23214568X-RAY DIFFRACTION99
3.021-3.09130.2865320.22524579X-RAY DIFFRACTION99
3.0913-3.16860.28935140.22264597X-RAY DIFFRACTION99
3.1686-3.25420.27015010.23054624X-RAY DIFFRACTION99
3.2542-3.350.26885110.22654596X-RAY DIFFRACTION99
3.35-3.45810.27075190.22224645X-RAY DIFFRACTION99
3.4581-3.58160.24284890.21014610X-RAY DIFFRACTION99
3.5816-3.7250.2545140.20424658X-RAY DIFFRACTION99
3.725-3.89440.23465320.19394580X-RAY DIFFRACTION99
3.8944-4.09970.21945100.19014646X-RAY DIFFRACTION99
4.0997-4.35640.2165160.18274615X-RAY DIFFRACTION99
4.3564-4.69250.22755050.19224669X-RAY DIFFRACTION99
4.6925-5.16420.22185070.19534674X-RAY DIFFRACTION100
5.1642-5.91030.2295310.20414663X-RAY DIFFRACTION100
5.9103-7.4420.22295130.19184733X-RAY DIFFRACTION100
7.442-48.27890.19455230.15864710X-RAY DIFFRACTION99

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