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- PDB-4nji: Crystal Structure of QueE from Burkholderia multivorans in comple... -

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Basic information

Entry
Database: PDB / ID: 4nji
TitleCrystal Structure of QueE from Burkholderia multivorans in complex with AdoMet, 6-carboxy-5,6,7,8-tetrahydropterin, and Mg2+
Components7-carboxy-7-deazaguanine synthase
KeywordsLYASE / AdoMet radical enzyme / modified partial TIM barrel-like structure / radical SAM fold / radical AdoMet fold / synthase
Function / homology
Function and homology information


7-carboxy-7-deazaguanine synthase / carbon-nitrogen lyase activity / tRNA queuosine(34) biosynthetic process / S-adenosyl-L-methionine binding / 4 iron, 4 sulfur cluster binding / magnesium ion binding / protein homodimerization activity / identical protein binding
Similarity search - Function
7-carboxy-7-deazaguanine synthase, Cx14CxxC-type / 7-carboxy-7-deazaguanine synthase-like / : / Radical SAM core domain profile. / Radical SAM / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-2K8 / PHOSPHATE ION / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / 7-carboxy-7-deazaguanine synthase / 7-carboxy-7-deazaguanine synthase
Similarity search - Component
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.197 Å
AuthorsDowling, D.P. / Bruender, N.A. / Young, A.P. / McCarty, R.M. / Bandarian, V. / Drennan, C.L.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism.
Authors: Dowling, D.P. / Bruender, N.A. / Young, A.P. / McCarty, R.M. / Bandarian, V. / Drennan, C.L.
History
DepositionNov 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Jul 2, 2014Group: Non-polymer description
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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.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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)52,87213
Polymers50,6872
Non-polymers2,18411
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-86 kcal/mol
Surface area17260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.126, 119.126, 104.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-429-

HOH

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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: 25343.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (bacteria) / Strain: ATCC 17616 / 249 / Gene: queE, Bmul_3115, BMULJ_00116 / Production host: Escherichia coli (E. coli)
References: UniProt: A9AC61, UniProt: A0A0H3KB22*PLUS, 7-carboxy-7-deazaguanine synthase

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Non-polymers , 7 types, 319 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-2K8 / (6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridine-6-carboxylic acid / 6-carboxy-5,6,7,8-tetrahydropterin


Mass: 211.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9N5O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: anaerobic, 1.8-2.2 M sodium dipotassium phosphate, pH 6.8, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2012
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.197→28.9 Å / Num. all: 38406 / Num. obs: 38406 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 36.2 Å2 / Rsym value: 0.102 / Net I/σ(I): 12.1
Reflection shellResolution: 2.197→2.28 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.459 / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NJG

4njg


Resolution: 2.197→28.892 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 18.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1801 1886 4.92 %
Rwork0.1527 --
obs0.1541 38352 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.197→28.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 113 308 3661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063466
X-RAY DIFFRACTIONf_angle_d0.974742
X-RAY DIFFRACTIONf_dihedral_angle_d13.7431300
X-RAY DIFFRACTIONf_chiral_restr0.035501
X-RAY DIFFRACTIONf_plane_restr0.005658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1974-2.25670.25371130.25922516X-RAY DIFFRACTION90
2.2567-2.32310.24751700.20072751X-RAY DIFFRACTION100
2.3231-2.39810.21331410.18062787X-RAY DIFFRACTION100
2.3981-2.48370.2171460.17142794X-RAY DIFFRACTION99
2.4837-2.58310.19721310.17132790X-RAY DIFFRACTION100
2.5831-2.70060.20431340.17832799X-RAY DIFFRACTION100
2.7006-2.84290.23381430.18032794X-RAY DIFFRACTION99
2.8429-3.02080.19621440.17572816X-RAY DIFFRACTION100
3.0208-3.25380.20191360.17792837X-RAY DIFFRACTION100
3.2538-3.58060.19371610.15382814X-RAY DIFFRACTION100
3.5806-4.09750.15311520.13152857X-RAY DIFFRACTION100
4.0975-5.15770.12951600.10842880X-RAY DIFFRACTION100
5.1577-28.89480.15991550.13733031X-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)
13.29220.15720.8971.33950.70861.3-0.0101-0.74940.25410.2119-0.09180.2511-0.0517-0.3350.07750.26620.04170.02230.4526-0.0680.2917-11.138385.625927.7891
23.87291.82453.7933.77332.33448.9640.1179-0.8374-0.12730.4535-0.24470.52480.4776-0.44520.13670.29030.01070.09930.5256-0.04230.4544-21.13879.49927.7192
32.84890.57790.84952.12030.16973.2704-0.1748-1.03610.35070.39290.05820.0419-0.2044-0.30740.09330.37840.038-0.01530.5595-0.13490.3225-7.883192.152233.4476
42.78390.7572.52241.00351.38156.3787-0.258-0.51340.57610.1673-0.06070.2291-0.5248-0.19690.31230.32710.0465-0.03420.3651-0.14450.4204-13.587496.150122.2516
51.9918-1.2123-0.43989.0783-2.82483.58130.01720.04120.10.1275-0.08450.0914-0.26350.00280.08540.19580.0159-0.04730.285-0.08930.2651-13.919787.0468.3692
62.09087.699-6.40612.0818-4.68216.9143-0.2780.6336-0.46290.00540.392-0.54060.24020.0220.00130.29780.0497-0.03680.3796-0.09820.374-8.246575.10475.5554
72.7649-0.5392-0.0455.3058-5.87148.38020.06640.1001-0.254-0.10330.12210.19120.160.2032-0.23130.2169-0.0185-0.02570.2684-0.07890.2895-4.648381.933310.8352
87.98920.23412.08730.8704-0.88151.40060.13890.6489-0.0446-0.1891-0.0113-0.2220.10750.3611-0.13770.28290.00010.0070.3988-0.10440.289313.417983.46071.7832
92.2571-0.7692.43316.4536-2.44737.37990.18490.852-0.3699-0.4943-0.2534-0.63930.77620.69510.04340.29130.03520.08470.5773-0.14230.522.106277.7740.988
104.4273-0.61353.06372.2336-0.00024.7779-0.09190.84960.1855-0.44550.0504-0.1301-0.21420.52020.04040.2918-0.04030.01570.4240.01890.221912.788192.008-1.4217
118.7265-6.6413.58826.1297-5.37557.9933-0.136-0.1130.45110.1875-0.1249-0.4731-0.73930.21070.18740.3025-0.0569-0.07960.249-0.06770.320813.796396.04778.0657
126.00882.59030.30754.2133-1.51762.7378-0.1293-0.1158-0.07020.10060.0483-0.2465-0.15810.02310.0770.21590.0097-0.03580.2508-0.0580.206917.944387.923819.5786
132.1195-8.8447-9.3339.55796.70279.2802-0.1631-0.5118-0.5522-0.07650.01550.65780.6716-0.24980.10730.3167-0.0742-0.11780.32830.05570.417310.279173.319323.4755
144.2991-0.40590.34144.79384.44612.2919-0.025-0.2165-0.2695-0.13850.0170.0377-0.0661-0.5309-0.00030.2688-0.0251-0.0410.28860.02650.27266.644981.718319.1845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:36)
2X-RAY DIFFRACTION2(chain A and resid 37:65)
3X-RAY DIFFRACTION3(chain A and resid 66:99)
4X-RAY DIFFRACTION4(chain A and resid 100:147)
5X-RAY DIFFRACTION5(chain A and resid 148:179)
6X-RAY DIFFRACTION6(chain A and resid 180:189)
7X-RAY DIFFRACTION7(chain A and resid 190:210)
8X-RAY DIFFRACTION8(chain B and resid 2:36)
9X-RAY DIFFRACTION9(chain B and resid 37:68)
10X-RAY DIFFRACTION10(chain B and resid 69:124)
11X-RAY DIFFRACTION11(chain B and resid 125:132)
12X-RAY DIFFRACTION12(chain B and resid 133:176)
13X-RAY DIFFRACTION13(chain B and resid 177:189)
14X-RAY DIFFRACTION14(chain B and resid 190:210)

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