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

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Basic information

Entry
Database: PDB / ID: 4njg
TitleCrystal Structure of QueE from Burkholderia multivorans in complex with AdoMet and 6-carboxypterin
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 / queuosine 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
6-CARBOXYPTERIN / 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 / Fe-SAD / Resolution: 2.598 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 1.3Feb 28, 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 / 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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_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)52,6028
Polymers50,6872
Non-polymers1,9146
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-21 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.956, 118.956, 101.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#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
#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-HHS / 6-CARBOXYPTERIN / 2-amino-4-oxo-3,4-dihydropteridine-6-carboxylic acid


Mass: 207.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5N5O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.56 Å3/Da / Density % sol: 65.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: anaerobic, 2.0 M sodium dipotassium phosphate, pH 6.8, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.598→47.2 Å / Num. all: 22950 / Num. obs: 22950 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 52 Å2 / Rsym value: 0.067 / Net I/σ(I): 18
Reflection shellResolution: 2.598→2.69 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.536 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CBASSdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Fe-SAD / Resolution: 2.598→47.164 Å / SU ML: 0.32 / σ(F): 1.36 / Phase error: 23.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 1145 5 %
Rwork0.1826 --
obs0.184 22885 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.598→47.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 100 104 3444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023434
X-RAY DIFFRACTIONf_angle_d0.6024694
X-RAY DIFFRACTIONf_dihedral_angle_d10.9271282
X-RAY DIFFRACTIONf_chiral_restr0.025498
X-RAY DIFFRACTIONf_plane_restr0.003666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5979-2.71610.28771500.26712662X-RAY DIFFRACTION99
2.7161-2.85930.29281260.24942669X-RAY DIFFRACTION98
2.8593-3.03840.30951380.24272687X-RAY DIFFRACTION100
3.0384-3.27290.26171320.22622730X-RAY DIFFRACTION100
3.2729-3.60220.21141590.19322651X-RAY DIFFRACTION98
3.6022-4.12310.18161420.15712745X-RAY DIFFRACTION100
4.1231-5.19370.15761520.13222735X-RAY DIFFRACTION99
5.1937-47.17170.19921460.17622861X-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)
13.62610.30991.55881.09240.31330.63820.0286-0.96040.37460.3632-0.24210.3726-0.1235-0.57720.17980.4360.04110.04030.7599-0.10920.4087-11.708785.460527.6953
26.55093.77716.66583.77921.86568.97890.1569-1.028-0.08740.6695-0.31850.44480.6835-0.53790.23390.47660.06150.13560.8174-0.10810.5997-21.721679.12227.8093
30.18260.39750.43842.94820.85633.7178-0.1599-1.39850.69790.6411-0.03140.0348-0.3175-0.41180.12610.58410.02180.00250.9248-0.25760.4536-8.607392.133333.3123
41.13390.77372.07910.65681.14165.1619-0.3851-0.70.8120.1816-0.10750.276-0.5689-0.25920.48480.47980.1058-0.06580.6326-0.28370.6388-14.590695.889922.091
50.3705-1.5365-0.00899.0017-0.97844.24330.0557-0.17940.035-0.0903-0.16940.3992-0.3494-0.21740.10860.23430.0314-0.04380.3809-0.09420.4333-14.736486.58778.3818
69.40596.1133-7.74438.3943-0.61362.0216-0.78690.4956-1.23320.71260.2688-1.15760.06580.08010.52590.360.0646-0.11830.4004-0.130.588-8.890474.75715.7019
74.1385-1.87611.19133.0518-4.07529.3490.14310.0168-0.16550.05860.02970.28240.11380.0662-0.15210.2742-0.03190.00410.2672-0.07910.4728-5.563381.662710.5742
87.20251.23552.40581.7623-0.27523.06230.03880.3844-0.0235-0.08540.0423-0.2706-0.13880.6529-0.06360.3519-0.0191-0.01060.5205-0.06410.363512.463383.61061.5884
94.1814-0.58692.90994.9636-2.07267.83940.23160.9955-0.5713-0.6232-0.1286-0.48170.55210.7897-0.07090.41690.04180.09520.6823-0.18030.555421.385277.99080.821
103.95650.25172.34142.6580.74813.782-0.10140.87840.2548-0.52540.15040.0179-0.44080.3783-0.06490.4497-0.03290.01080.63150.05730.34811.704192.1117-1.7603
112.0216-7.44674.03988.3647-7.02146.9938-0.2793-0.20991.22460.5347-0.4988-1.0828-0.60650.590.60980.3795-0.051-0.13040.4294-0.03190.591712.791596.35767.666
125.51341.97180.79187.223-2.83034.666-0.0271-0.17260.04980.4685-0.09-0.3359-0.43710.04940.12610.2620.0121-0.05280.2988-0.08010.328417.182988.360719.176
132.09061.8756-8.66777.2845.23117.6439-0.5853-0.9975-1.39210.06630.38561.03340.7318-0.2401-0.01010.3925-0.0246-0.21660.44770.07260.62239.916373.672523.1542
144.41922.09144.25957.09064.14075.3368-0.0155-0.3032-0.3296-0.10410.05970.2134-0.1505-0.20860.03980.3028-0.00030.05560.4322-0.040.43756.0981.494118.9095
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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