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- PDB-6nhl: Crystal structure of QueE from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 6nhl
TitleCrystal structure of QueE from Escherichia coli
Components7-carboxy-7-deazaguanine synthase
KeywordsLYASE / AdoMet radical enzyme / AdoMet radical fold / Sam radical fold / 7-carboxy-7-deazaguanine synthase / AdoMet / Iron-sulfur cluster / metalloprotein
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
Similarity search - Function
Putative 7-carboxy-7-deazaguanine synthase QueE, Proteobacteria / 7-carboxy-7-deazaguanine synthase-like / : / Radical SAM superfamily / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / 7-carboxy-7-deazaguanine synthase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.101 Å
AuthorsGrell, T.A.J. / Bell, B.N. / Nguyen, C. / Dowling, D.P. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1122374 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35 GM126982 R01 GM72623 R35 GM126956 and R35 GM126982 United States
CitationJournal: Protein Sci. / Year: 2019
Title: Crystal structure of AdoMet radical enzyme 7-carboxy-7-deazaguanine synthase from Escherichia coli suggests how modifications near [4Fe-4S] cluster engender flavodoxin specificity.
Authors: Grell, T.A.J. / Bell, B.N. / Nguyen, C. / Dowling, D.P. / Bruender, N.A. / Bandarian, V. / Drennan, C.L.
History
DepositionDec 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Refinement description / Category: refine / reflns_shell / Item: _refine.details / _reflns_shell.number_unique_all
Revision 1.2May 8, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)55,8128
Polymers54,8302
Non-polymers9826
Water6,215345
1
A: 7-carboxy-7-deazaguanine synthase
hetero molecules

B: 7-carboxy-7-deazaguanine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8128
Polymers54,8302
Non-polymers9826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area2400 Å2
ΔGint-64 kcal/mol
Surface area21410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.264, 74.493, 103.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 27415.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: queE, EC1303_c28920 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0E1M5B1, 7-carboxy-7-deazaguanine synthase

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Non-polymers , 6 types, 351 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: Anaerobic, 175-200 mM Magnesium chloride, 25-30% PEG 400 and Tris HCl pH 8.5
PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.7384, 0.972
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.73841
20.9721
ReflectionResolution: 2.1→46 Å / Num. obs: 31076 / % possible obs: 96 % / Redundancy: 8.6 % / Rsym value: 0.153 / Net I/σ(I): 17.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 2456 / CC1/2: 0.879 / Rsym value: 0.489 / % possible all: 76

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
HKL2Mapphasing
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 2.101→45.848 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.51
Details: Electron density observed near the unique iron of the iron sulfur clusters could not be confidently fitted, but may represent disordered S-adenosy-L-methionine
RfactorNum. reflection% reflection
Rfree0.2263 1874 6.45 %
Rwork0.1726 --
obs0.1761 29065 89.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.101→45.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 31 345 3896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033662
X-RAY DIFFRACTIONf_angle_d0.5394987
X-RAY DIFFRACTIONf_dihedral_angle_d22.8081351
X-RAY DIFFRACTIONf_chiral_restr0.062559
X-RAY DIFFRACTIONf_plane_restr0.004638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1014-2.15820.329970.23991368X-RAY DIFFRACTION60
2.1582-2.22170.31441000.21011649X-RAY DIFFRACTION72
2.2217-2.29340.28121310.21421790X-RAY DIFFRACTION78
2.2934-2.37540.31921290.1982003X-RAY DIFFRACTION86
2.3754-2.47050.28471410.18142070X-RAY DIFFRACTION90
2.4705-2.58290.22051520.18012139X-RAY DIFFRACTION93
2.5829-2.71910.25861470.18952208X-RAY DIFFRACTION95
2.7191-2.88940.24311630.18972209X-RAY DIFFRACTION96
2.8894-3.11250.23871460.18422296X-RAY DIFFRACTION97
3.1125-3.42560.22631660.17842282X-RAY DIFFRACTION98
3.4256-3.92110.21331630.15622346X-RAY DIFFRACTION99
3.9211-4.93920.15421690.12842350X-RAY DIFFRACTION100
4.9392-45.85920.21011700.16792481X-RAY DIFFRACTION99
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)
10.23750.2227-0.08650.9673-0.10460.4525-0.02020.0190.0181-0.1969-0.0186-0.0466-0.022-0.0152-0.05440.1320.00040.01510.10730.00520.077660.673511.17559.4613
20.1681-0.0092-0.16891.218-0.1760.21410.03960.00210.00120.0585-0.03460.0283-0.0111-0.03280.03230.0836-0.00080.0120.1216-0.00090.103449.5637-17.042773.745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 210 )
2X-RAY DIFFRACTION2chain 'B' and (resid 12 through 210 )

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