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- PDB-6p78: queuine lyase from Clostridium spiroforme bound to SAM and queuine -

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Basic information

Entry
Database: PDB / ID: 6p78
Titlequeuine lyase from Clostridium spiroforme bound to SAM and queuine
ComponentsQueuine lyase
KeywordsLYASE / Metal Ion Binding / 4 Iron 4 Sulfur Cluster Binding / Radical SAM enzyme / C-N lyase activity
Function / homologyElp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / iron-sulfur cluster binding / catalytic activity / metal ion binding / Chem-QUG / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / Radical SAM domain protein
Function and homology information
Biological species[Clostridium] spiroforme DSM 1552 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.726 Å
AuthorsAlmo, S.C. / Grove, T.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI133329 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54-GM093342 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens.
Authors: Yuan, Y. / Zallot, R. / Grove, T.L. / Payan, D.J. / Martin-Verstraete, I. / Sepic, S. / Balamkundu, S. / Neelakandan, R. / Gadi, V.K. / Liu, C.F. / Swairjo, M.A. / Dedon, P.C. / Almo, S.C. / ...Authors: Yuan, Y. / Zallot, R. / Grove, T.L. / Payan, D.J. / Martin-Verstraete, I. / Sepic, S. / Balamkundu, S. / Neelakandan, R. / Gadi, V.K. / Liu, C.F. / Swairjo, M.A. / Dedon, P.C. / Almo, S.C. / Gerlt, J.A. / de Crecy-Lagard, V.
History
DepositionJun 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Queuine lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9614
Polymers29,9341
Non-polymers1,0273
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.606, 57.606, 152.414
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Queuine lyase / Radical SAM domain protein


Mass: 29934.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Clostridium] spiroforme DSM 1552 (bacteria)
Gene: CLOSPI_01524 / Plasmid: pSGC-His / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1C2R2
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-QUG / 2-amino-5-({[(1S,4S,5S)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-1,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one / Queuine / Queuine


Mass: 277.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1 M CHES, pH 9.5, 30% polyethylene glycol 3,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1.3776 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3776 Å / Relative weight: 1
ReflectionResolution: 1.69→53.89 Å / Num. obs: 29732 / % possible obs: 100 % / Redundancy: 27.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.023 / Rrim(I) all: 0.117 / Net I/σ(I): 19.4 / Num. measured all: 814983 / Scaling rejects: 1
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
1.69-1.7827.61.63811697142360.9050.3161.6692.7100
5.35-53.8922.50.0662457210930.9980.0140.06848.299.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimless0.7.1data scaling
AutoSol1.14-3260phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.726→28.803 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.28 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1996 2000 7.17 %
Rwork0.1651 25880 -
obs0.1676 27880 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.04 Å2 / Biso mean: 32.7345 Å2 / Biso min: 15.58 Å2
Refinement stepCycle: final / Resolution: 1.726→28.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 55 221 2207
Biso mean--31.75 40.4 -
Num. residues----230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7263-1.76940.24491420.217418271969
1.7694-1.81730.25111380.213817971935
1.8173-1.87070.21911400.184418081948
1.8707-1.93110.21221400.175718121952
1.9311-2.00010.2081390.172218051944
2.0001-2.08020.21221400.176818181958
2.0802-2.17480.2031410.173118121953
2.1748-2.28940.23191430.16618421985
2.2894-2.43280.25071420.17118471989
2.4328-2.62050.20681430.176418541997
2.6205-2.8840.20221440.174718501994
2.884-3.30080.21011440.167118672011
3.3008-4.15670.19061480.148619152063
4.1567-28.8070.16421560.153320262182
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)
13.5477-1.8179-0.58056.9295-0.11927.3811-0.0892-0.0462-0.25390.4354-0.11970.28560.1966-0.6270.22540.1794-0.0386-0.01250.1760.00780.17948.651834.088980.2887
21.3263-0.59620.80282.7104-0.48625.0695-0.0691-0.03690.20930.17520.0388-0.0229-0.8041-0.32010.01620.35950.0488-0.02620.1837-0.01210.18485.272451.446669.1309
30.581-0.1284-0.05497.5071.24830.3107-0.4359-0.48680.23310.81370.3280.0057-1.6421-0.60420.20860.74850.0469-0.00720.3188-0.03450.25858.057950.326383.3527
42.9644-0.64450.62594.605-0.34653.3191-0.0308-0.2360.1210.0547-0.0286-0.0852-0.41810.00250.02810.2176-0.0154-0.02630.13360.00380.129614.659741.387578.3621
56.3384-2.4002-1.676.42991.23070.5247-0.2277-0.41620.77380.45690.1475-0.885-0.92660.84070.00770.594-0.1501-0.18910.3301-0.00410.374721.61946.198884.1366
62.64170.06370.70623.7993-0.58556.30270.0798-0.2371-0.2160.2174-0.0411-0.010.01740.125-0.08880.1964-0.0514-0.02920.13920.04170.177719.025738.016375.7565
75.6477-2.29133.81344.5646-3.52887.2769-0.07810.22920.20750.076-0.2351-0.3666-0.41910.69560.39090.2816-0.0767-0.04560.17080.02970.209523.01247.528867.7266
85.1634-1.70152.37752.163-1.3323.78320.110.24660.044-0.2341-0.1343-0.07610.02860.07510.0140.2214-0.021-0.00790.0661-0.00640.171112.478143.038958.1037
97.4164-0.54731.25770.8486-0.40532.9101-0.06690.25-0.09780.00520.03310.01060.1587-0.05740.04090.2489-0.0182-0.01620.08040.00610.17047.995235.154956.2183
104.7473-1.5117-0.28661.647-0.05453.2232-0.0728-0.4017-0.22610.1950.11040.07380.3401-0.3619-0.05210.265-0.0557-0.01380.1920.01050.21951.204131.984964.6332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 17 )A0 - 17
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 32 )A18 - 32
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 54 )A33 - 54
4X-RAY DIFFRACTION4chain 'A' and (resid 55 through 74 )A55 - 74
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 87 )A75 - 87
6X-RAY DIFFRACTION6chain 'A' and (resid 88 through 98 )A88 - 98
7X-RAY DIFFRACTION7chain 'A' and (resid 99 through 112 )A99 - 112
8X-RAY DIFFRACTION8chain 'A' and (resid 113 through 147 )A113 - 147
9X-RAY DIFFRACTION9chain 'A' and (resid 148 through 177 )A148 - 177
10X-RAY DIFFRACTION10chain 'A' and (resid 178 through 229 )A178 - 229

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