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- PDB-5k0p: Crystal structure of the archaeosine synthase QueF-Like in the ap... -

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Basic information

Entry
Database: PDB / ID: 5k0p
TitleCrystal structure of the archaeosine synthase QueF-Like in the apo form
ComponentsArcheaosine synthase QueF-Like
KeywordsTRANSFERASE / Amidinotransferase / Tunneling-fold enzyme / P2 structure
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
TRIETHYLENE GLYCOL / THIOCYANATE ION / Archaeosine synthase
Similarity search - Component
Biological speciesPyrobaculum calidifontis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 17, 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 1.4Sep 27, 2023Group: 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,93624
Polymers120,71110
Non-polymers1,22614
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23010 Å2
ΔGint-113 kcal/mol
Surface area41090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.210, 124.995, 74.404
Angle α, β, γ (deg.)90.000, 112.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Archeaosine synthase QueF-Like


Mass: 12071.085 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum calidifontis (strain JCM 11548 / VA1) (archaea)
Strain: JCM 11548 / VA1 / Gene: Pcal_0221 / Production host: Escherichia coli (E. coli) / References: UniProt: A3MSP1
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 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: Nov 22, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97607 Å / Relative weight: 1
ReflectionResolution: 1.94→69 Å / Num. obs: 77458 / % possible obs: 99.8 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 8.1
Reflection shellResolution: 1.94→1.98 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 1.8 / Num. unique all: 4850 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JYX

5jyx


Resolution: 1.94→69 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.946 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 3886 5 %RANDOM
Rwork0.1546 ---
obs0.1589 73364 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.23 Å2 / Biso mean: 35.243 Å2 / Biso min: 15.42 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å2-0 Å2-0.31 Å2
2--0.47 Å20 Å2
3---0.86 Å2
Refinement stepCycle: final / Resolution: 1.94→69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7811 0 73 436 8320
Biso mean--66.16 38.35 -
Num. residues----1008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0198168
X-RAY DIFFRACTIONr_bond_other_d0.0020.028167
X-RAY DIFFRACTIONr_angle_refined_deg2.2472.00811045
X-RAY DIFFRACTIONr_angle_other_deg1.1053.00118950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56851035
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89923.856306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.921151491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5481553
X-RAY DIFFRACTIONr_chiral_restr0.1260.21300
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218807
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021538
X-RAY DIFFRACTIONr_mcbond_it4.2532.4414088
X-RAY DIFFRACTIONr_mcbond_other4.1312.4274077
X-RAY DIFFRACTIONr_mcangle_it4.7483.6115096
X-RAY DIFFRACTIONr_rigid_bond_restr5.447316335
X-RAY DIFFRACTIONr_sphericity_free27.4365162
X-RAY DIFFRACTIONr_sphericity_bonded11.835516457
LS refinement shellResolution: 1.937→1.987 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 258 -
Rwork0.216 4850 -
all-5108 -
obs--89.33 %
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)
11.1475-0.8691-0.59551.58760.67830.9503-0.03630.068-0.0175-0.0072-0.0950.15350.1016-0.11380.13130.0417-0.0223-0.01010.0203-0.00550.0596-10.758-30.105-12.06
21.80540.3103-0.41920.7429-0.16850.713-0.0501-0.06940.00180.1253-0.0527-0.08390.09330.06690.10280.0659-0.0022-0.01610.01050.00830.059215.934-30.388-1.644
31.2618-0.71340.26931.5649-0.04490.36490.03970.03140.02550.2084-0.0676-0.0613-0.03010.02880.02780.0907-0.0127-0.0340.0063-0.00040.039313.627-6.6529.395
41.1467-0.59480.33330.9347-0.24140.70130.00190.0321-0.01860.18510.01130.12410.0101-0.0331-0.01320.075-0.00340.02870.01020.01080.0763-13.497-8.0691.453
52.75770.4789-0.75270.93550.01160.7324-0.19450.21570.0178-0.23360.13260.03180.0254-0.08440.06190.1064-0.0522-0.01970.03660.00710.0224-2.302-23.897-36.371
61.07240.78480.56631.28580.34780.81020.0161-0.11250.0536-0.26490.02560.0739-0.0567-0.1241-0.04170.1484-0.0451-0.02650.03940.01920.04090.2442.326-37.359
70.8708-0.3770.99271.1931-0.1291.7869-0.02730.08910.08970.05330.0859-0.0286-0.16510.1402-0.05860.0602-0.01690.01040.04260.03880.102420.66211.846-7.762
81.0282-0.0587-0.55930.47850.48312.60050.10010.20920.10910.0529-0.0137-0.0039-0.2121-0.3491-0.08640.05090.0460.00670.07190.02870.0535-6.62212.362-13.986
91.79680.560.38291.05780.31540.2035-0.04170.0331-0.0331-0.0808-0.0253-0.10370.02470.04460.0670.06590.03160.0450.03950.05220.133224.329-26.771-26.482
101.32210.44840.49130.89410.72241.8789-0.07-0.0681-0.0878-0.22050.1173-0.0358-0.16340.2287-0.04730.0665-0.0474-0.01340.070.02950.042427.204-1.14-30.456
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 108
2X-RAY DIFFRACTION2B6 - 105
3X-RAY DIFFRACTION3C6 - 105
4X-RAY DIFFRACTION4D6 - 106
5X-RAY DIFFRACTION5E6 - 105
6X-RAY DIFFRACTION6F6 - 106
7X-RAY DIFFRACTION7G6 - 106
8X-RAY DIFFRACTION8H6 - 104
9X-RAY DIFFRACTION9I6 - 107
10X-RAY DIFFRACTION10J6 - 105

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