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- PDB-5tgs: Crystal Structure of QueE from Bacillus subtilis with methionine bound -

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Basic information

Entry
Database: PDB / ID: 5tgs
TitleCrystal Structure of QueE from Bacillus subtilis with methionine bound
Components7-carboxy-7-deazaguanine synthase
KeywordsLYASE / S-Adenosylmethionine radical enzyme / 7-Carboxy-7-deazaguanine synthase
Function / homology
Function and homology information


7-carboxy-7-deazaguanine synthase / carbon-nitrogen lyase activity / queuosine biosynthetic process / S-adenosyl-L-methionine binding / 4 iron, 4 sulfur cluster binding / magnesium ion binding / protein homodimerization activity
Similarity search - Function
7-carboxy-7-deazaguanine synthase / 7-carboxy-7-deazaguanine synthase-like / : / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
METHIONINE / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / 7-carboxy-7-deazaguanine synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.548 Å
AuthorsGrell, T.A.J. / Dowling, D.P. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM72623 United States
National Science Foundation (NSF, United States)1122374 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: 7-Carboxy-7-deazaguanine Synthase: A Radical S-Adenosyl-l-methionine Enzyme with Polar Tendencies.
Authors: Bruender, N.A. / Grell, T.A. / Dowling, D.P. / McCarty, R.M. / Drennan, C.L. / Bandarian, V.
History
DepositionSep 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 7-carboxy-7-deazaguanine synthase
B: 7-carboxy-7-deazaguanine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6056
Polymers58,6472
Non-polymers9594
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-56 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.182, 79.297, 122.224
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 7-carboxy-7-deazaguanine synthase / CDG synthase / Queuosine biosynthesis protein QueE


Mass: 29323.311 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: queE, ykvL, BSU13740 / Production host: Escherichia coli (E. coli)
References: UniProt: O31677, 7-carboxy-7-deazaguanine synthase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe4S4
#3: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C5H11NO2S
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 MTris HCl (pH 8.5), 22% PEG 8000 and 0.1 M Magnesium chloride
PH range: 7.4-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9999 , 1.7389
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 29, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.99991
21.73891
ReflectionResolution: 2.548→50 Å / Num. obs: 17745 / % possible obs: 99.3 % / Redundancy: 3.9 % / Rsym value: 0.07 / Net I/σ(I): 17.7
Reflection shellResolution: 2.548→2.64 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.3 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
SHARPphasing
autoSHARPphasing
AutoSolphasing
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.548→42.011 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.68
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 836 4.72 %Random selection
Rwork0.2158 ---
obs0.2173 17694 99.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.548→42.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3627 0 32 85 3744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0763753
X-RAY DIFFRACTIONf_angle_d2.1285116
X-RAY DIFFRACTIONf_dihedral_angle_d11.9792223
X-RAY DIFFRACTIONf_chiral_restr0.04576
X-RAY DIFFRACTIONf_plane_restr0.003643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5477-2.70730.34771340.28852735X-RAY DIFFRACTION98
2.7073-2.91630.28991200.2652800X-RAY DIFFRACTION100
2.9163-3.20970.26561530.26062766X-RAY DIFFRACTION100
3.2097-3.67390.24511280.22622803X-RAY DIFFRACTION100
3.6739-4.62780.21871590.18852818X-RAY DIFFRACTION99
4.6278-42.01630.2431420.19262936X-RAY DIFFRACTION98
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)
10.19410.1737-0.08520.1401-0.07150.033-0.2346-0.1127-0.03480.01720.09180.10290.3649-0.0527-0.00020.3980.04160.0140.44190.00110.513124.162444.537150.1054
21.4914-0.93280.17452.6425-0.02331.534-0.0088-0.0433-0.07220.0699-0.07150.18270.1413-0.11200.3486-0.04560.00340.3698-0.01580.389622.504835.6515152.4835
30.1281-0.165-0.28960.3480.02851.2934-0.1309-0.0738-0.00610.07940.0336-0.18550.34410.2253-0.05390.2176-0.0133-0.03230.41950.03670.453443.373632.9753150.5239
40.1718-0.1047-0.0230.1193-0.15070.39240.1603-0.06310.27880.3056-0.1115-0.0701-0.12510.1024-0.00010.4632-0.03640.02210.54950.07840.618139.321337.4189148.4657
50.10050.05750.04610.04210.00170.09140.30420.0097-0.1546-0.41770.1862-0.3502-0.58810.444-0.00020.70220.01410.11340.64340.07180.541951.105135.8706126.7928
60.26150.0213-0.15560.0728-0.04180.08880.1851-0.14410.5854-0.0713-0.1093-0.0884-0.06930.0684-0.00080.64330.03960.18580.59410.11820.575445.949242.7282127.0193
70.4967-0.0025-0.08940.090.0150.3322-0.00330.1154-0.0298-0.4096-0.1513-0.40050.090.65930.00010.67780.11710.18980.79090.09160.632856.320835.0221121.2638
80.76480.2083-0.23050.23260.11110.27440.06240.2761-0.2282-0.5373-0.0277-0.17030.2278-0.40710.00690.7430.10510.11510.6020.09250.457743.650531.572123.1727
91.0301-0.3939-0.59690.20560.23380.38160.44230.3998-0.1506-0.4446-0.5038-0.12520.0678-0.5751-0.00050.6890.03880.03610.61260.00570.541433.545542.4087121.7816
100.5172-0.4975-0.35580.4760.35890.44680.36140.37350.0324-0.3625-0.18440.2293-0.5201-0.20070.01920.64880.07370.110.55170.09850.571932.425551.9117129.4658
110.43360.11481.14040.05510.23653.1621-0.2176-0.15510.25060.00820.0649-0.8977-0.4121-0.0737-0.10960.6202-0.1213-0.01540.35210.02810.839938.853156.1153141.6741
120.5427-0.615-0.25350.69850.3130.43980.14680.1674-0.205-0.467-0.10420.0623-0.34880.07330.05130.3999-0.0880.08430.49860.03870.541537.638448.6708137.8468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 166 )
3X-RAY DIFFRACTION3chain 'A' and (resid 167 through 218 )
4X-RAY DIFFRACTION4chain 'A' and ((resid 219 through 237 ) or resid 302)
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 18 )
6X-RAY DIFFRACTION6chain 'B' and (resid 19 through 43 )
7X-RAY DIFFRACTION7chain 'B' and (resid 44 through 70 )
8X-RAY DIFFRACTION8chain 'B' and (resid 71 through 115 )
9X-RAY DIFFRACTION9chain 'B' and (resid 116 through 166 )
10X-RAY DIFFRACTION10chain 'B' and (resid 167 through 201 )
11X-RAY DIFFRACTION11chain 'B' and (resid 202 through 218 )
12X-RAY DIFFRACTION12chain 'B' and (resid 219 through 239 )

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