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- PDB-5jyx: Crystal structure of the covalent thioimide intermediate of the a... -

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Basic information

Entry
Database: PDB / ID: 5jyx
TitleCrystal structure of the covalent thioimide intermediate of the archaeosine synthase QueF-Like
ComponentsArcheaosine synthase QueF-Like
KeywordsTRANSFERASE / thioimide / amidinotransferase / C2 space group / HYDROLASE
Function / homology
Function and homology information


preQ1 synthase activity / Transferases; Transferring nitrogenous groups; Transaminases / queuosine biosynthetic process / tRNA processing / transferase activity
Similarity search - Function
NADPH-dependent 7-cyano-7-deazaguanine reductase QueF / QueF-like protein / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase
Similarity search - Domain/homology
Chem-GD1 / Archaeosine synthase
Similarity search - Component
Biological speciesPyrobaculum calidifontis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsMei, X. / Swairjo, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE- 1309323 United States
CitationJournal: Proteins / Year: 2017
Title: Crystal structure of the archaeosine synthase QueF-like-Insights into amidino transfer and tRNA recognition by the tunnel fold.
Authors: Mei, X. / Alvarez, J. / Bon Ramos, A. / Samanta, U. / Iwata-Reuyl, D. / Swairjo, M.A.
History
DepositionMay 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 29, 2020Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_prop.value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Archeaosine synthase QueF-Like
B: Archeaosine synthase QueF-Like
C: Archeaosine synthase QueF-Like
D: Archeaosine synthase QueF-Like
E: Archeaosine synthase QueF-Like
F: Archeaosine synthase QueF-Like
G: Archeaosine synthase QueF-Like
H: Archeaosine synthase QueF-Like
I: Archeaosine synthase QueF-Like
J: Archeaosine synthase QueF-Like
K: Archeaosine synthase QueF-Like
L: Archeaosine synthase QueF-Like
M: Archeaosine synthase QueF-Like
N: Archeaosine synthase QueF-Like
O: Archeaosine synthase QueF-Like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,20033
Polymers182,47315
Non-polymers2,72618
Water2,288127
1
A: Archeaosine synthase QueF-Like
C: Archeaosine synthase QueF-Like
J: Archeaosine synthase QueF-Like
M: Archeaosine synthase QueF-Like
N: Archeaosine synthase QueF-Like
hetero molecules

A: Archeaosine synthase QueF-Like
C: Archeaosine synthase QueF-Like
J: Archeaosine synthase QueF-Like
M: Archeaosine synthase QueF-Like
N: Archeaosine synthase QueF-Like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,46622
Polymers121,64910
Non-polymers1,81812
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area22480 Å2
ΔGint-140 kcal/mol
Surface area38820 Å2
MethodPISA
2
B: Archeaosine synthase QueF-Like
D: Archeaosine synthase QueF-Like
E: Archeaosine synthase QueF-Like
F: Archeaosine synthase QueF-Like
G: Archeaosine synthase QueF-Like
H: Archeaosine synthase QueF-Like
I: Archeaosine synthase QueF-Like
K: Archeaosine synthase QueF-Like
L: Archeaosine synthase QueF-Like
O: Archeaosine synthase QueF-Like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,46622
Polymers121,64910
Non-polymers1,81812
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22370 Å2
ΔGint-138 kcal/mol
Surface area41100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.325, 126.779, 65.083
Angle α, β, γ (deg.)90.000, 102.580, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Archeaosine synthase QueF-Like


Mass: 12164.875 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum calidifontis (archaea) / Strain: JCM 11548 / VA1 / Gene: Pcal_0221 / Production host: Escherichia coli (E. coli) / References: UniProt: A3MSP1
#2: Chemical
ChemComp-GD1 / 2-amino-5-[(Z)-iminomethyl]-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one / 7-cyano-7-deazaguanine, bound form


Mass: 177.163 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C7H7N5O
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 66 uM preQ0, 17-19% PEG3350, 0.15 M potassium thiocyanate, and 0.05% sodium azide.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97607 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 14, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97607 Å / Relative weight: 1
ReflectionResolution: 2.74→29 Å / Num. obs: 43893 / % possible obs: 98.7 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.5
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 3 / Num. unique all: 2172 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
PHENIXphasing
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→108.56 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.901 / SU B: 32.344 / SU ML: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 1975 4.6 %RANDOM
Rwork0.1711 ---
obs0.1752 41291 96.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 181.44 Å2 / Biso mean: 54.255 Å2 / Biso min: 15.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20.13 Å2
2---0.12 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 2.74→108.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12191 0 198 127 12516
Biso mean--56.02 42.38 -
Num. residues----1574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01912671
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212673
X-RAY DIFFRACTIONr_angle_refined_deg2.1492.0317145
X-RAY DIFFRACTIONr_angle_other_deg1.013.00129315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67551577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43523.837443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.532152271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7281576
X-RAY DIFFRACTIONr_chiral_restr0.0950.22021
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113594
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022404
X-RAY DIFFRACTIONr_mcbond_it2.2983.7956302
X-RAY DIFFRACTIONr_mcbond_other2.2983.7956301
X-RAY DIFFRACTIONr_mcangle_it3.9535.6657857
LS refinement shellResolution: 2.739→2.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 135 -
Rwork0.243 2789 -
all-2924 -
obs--87.99 %
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)
12.6852-1.2486-0.4721.58210.41580.61090.01160.07350.0825-0.03180.0103-0.1303-0.05840.0269-0.02180.08920.01610.02590.158-0.01180.081811.412682.529625.5372
20.5654-0.2444-0.35691.10610.81071.90370.0216-0.0289-0.07130.131-0.0449-0.0294-0.03520.06830.02330.15350.026-0.02260.10330.01010.10161.034845.177896.3248
33.3713-0.5316-0.18920.5849-0.05250.54450.0009-0.28570.10590.03510.0075-0.0903-0.0032-0.016-0.00840.1346-0.0249-0.02050.1735-0.04230.0292-1.955582.455750.4048
40.7055-0.23110.28450.9164-0.4091.28090.07490.0467-0.0581-0.0876-0.0730.07760.08220.0844-0.00190.18390.0862-0.02590.09480.0050.087454.973439.781257.3184
51.0551-0.18511.01330.31790.31922.12650.0818-0.1779-0.1815-0.0686-0.01740.00730.0644-0.1994-0.06440.08350.0109-0.01640.07290.05220.206940.547436.488981.4098
60.89450.1829-0.24022.1578-0.78250.8222-0.0869-0.12820.0134-0.06180.01610.2593-0.0340.03550.07080.07270.0596-0.01030.0832-0.02020.229625.923858.102476.0246
71.21471.0231-0.43342.7968-0.33170.6507-0.15720.13090.0027-0.14280.04430.0666-0.04210.01390.11290.20320.0339-0.07940.09390.04110.102340.530661.402651.4183
80.57570.21580.4911.15151.11732.77110.0410.2065-0.004-0.00290.045-0.1477-0.05850.446-0.0860.0240.01730.01590.25520.020.102176.377648.247571.2998
91.9465-1.1993-0.64710.98350.29791.1455-0.1469-0.07550.06830.1552-0.0119-0.0943-0.1374-0.00490.15880.21-0.0015-0.04920.0368-0.03520.116659.938771.06398.8579
100.9446-0.9657-0.44693.07611.24691.2585-0.2554-0.1942-0.26850.46890.1467-0.02880.1330.12480.10870.17350.02930.0040.14320.1030.15265.339456.995654.21
113.4560.99240.35920.3358-0.00571.25-0.13610.01830.2734-0.0767-0.04850.1335-0.13190.2340.18460.2035-0.0028-0.11160.07180.04460.226452.598382.792562.2725
122.5129-1.7658-1.03032.55891.52771.2341-0.22810.07210.2139-0.14970.0739-0.2507-0.23030.21030.15420.1565-0.1043-0.11680.10660.15620.293374.776174.552674.2746
130.5377-0.0559-0.58512.71581.81742.5456-0.0821-0.0628-0.2815-0.01340.0451-0.2529-0.1233-0.03720.0370.06190.06410.04780.1472-0.02450.223118.644757.563829.5446
141.4942-0.29622.03441.0776-0.52214.32640.33850.2607-0.4377-0.05740.04930.11290.20850.457-0.38770.12220.0136-0.05830.1034-0.1650.4157-0.334241.337719.4528
153.35121.52530.33520.87240.36641.04680.01-0.13750.21860.1192-0.08340.1581-0.1858-0.02680.07340.22020.0113-0.00750.0406-0.09110.211637.936979.442686.31
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 105
2X-RAY DIFFRACTION2B1 - 109
3X-RAY DIFFRACTION3C1 - 104
4X-RAY DIFFRACTION4D1 - 105
5X-RAY DIFFRACTION5E1 - 104
6X-RAY DIFFRACTION6F2 - 105
7X-RAY DIFFRACTION7G1 - 107
8X-RAY DIFFRACTION8H2 - 105
9X-RAY DIFFRACTION9I1 - 107
10X-RAY DIFFRACTION10J1 - 104
11X-RAY DIFFRACTION11K1 - 106
12X-RAY DIFFRACTION12L1 - 105
13X-RAY DIFFRACTION13M2 - 104
14X-RAY DIFFRACTION14N1 - 104
15X-RAY DIFFRACTION15O1 - 103

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